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GET vep/:species/hgvs/:hgvs_notation

Fetch variant consequences based on a HGVS notation

Parameters

Required

NameTypeDescriptionDefaultExample Values
hgvs_notation String HGVS notation. May be genomic (g), coding (c) or protein (p), with reference to chromosome name, gene name, transcript ID or protein ID. - ENST00000366667:c.803C>T
9:g.22125504G>C
ENST00000003084:c.1431_1433delTTC
species String Species name/alias - homo_sapiens
human

Optional

NameTypeDescriptionDefaultExample Values
AncestralAllele Boolean Retrieves the ancestral allele for variants inferred from the Ensembl Compara Enredo-Pecan-Ortheus (EPO) pipeline (plugin details) 0 -
Blosum62 Boolean Include BLOSUM62 amino acid conservation score (plugin details) 0 -
CADD Boolean Include CADD (Combined Annotation Dependent Depletion) deleteriousness scores for single nucleotide variants. See license. (plugin details) 0 -
Conservation Boolean Retrieves a conservation score from the Ensembl Compara databases for variant positions (plugin details) 0 -
DisGeNET Boolean Retrieves Variant-Disease-PMID associations from the DisGeNET database (plugin details) 0 -
EVE Boolean EVE (evolutionary model of variant effect) is a computational method for the classification of human genetic variants trained solely on evolutionary sequences. See license. (plugin details) 0 -
GO Boolean Retrieves Gene Ontology terms associated with transcripts/translations 0 -
GeneSplicer Boolean Detects splice sites in genomic DNA (plugin details) 0 -
IntAct Boolean Provides molecular interaction data for variants as reported by IntAct database. (plugin details) - -
LoF Boolean LOFTEE identifies LoF (loss-of-function) variation. See README for more details. 0 -
Mastermind Boolean Variants that have clinical evidence cited in the medical literature reported by Mastermind Genomic Search Engine (plugin details) 0 -
MaxEntScan Boolean Sequence motif and maximum entropy based splice site consensus predictions (plugin details) 0 -
Phenotypes Boolean Retrieves overlapping phenotype information (plugin details) 0 -
SpliceAI Integer Retrieves pre-calculated annotations from SpliceAI a deep neural network, developed by Illumina, Inc that predicts splice junctions from an arbitrary pre-mRNA transcript sequence. Used for non-commercial purposes. (plugin details)
The pre-calculated annotations for all possible single nucleotide substitutions can be retrieved from: value 1) Ensembl/GENCODE v24 canonical transcripts (masked scores); value 2) Ensembl/GENCODE v37 MANE transcripts (raw scores).
Note: The pre-calculated annotations for 1 base insertions, and 1-4 base deletions are only available for Ensembl/GENCODE v24 canonical transcripts.		 0 2
appris Boolean Include APPRIS isoform annotation 0 -
callback String Name of the callback subroutine to be returned by the requested JSONP response. Required ONLY when using JSONP as the serialisation method. Please see the user guide. - randomlygeneratedname
canonical Boolean Include a flag indicating the canonical transcript for a gene 0 -
ccds Boolean Include CCDS transcript identifiers 0 -
dbNSFP String Include fields from dbNSFP, a database of pathogenicity predictions for missense variants. Multiple fields should be separated by commas. See dbNSFP README for field list. (plugin details) Not used LRT_pred,MutationTaster_pred
dbscSNV Boolean Predictions for splicing variants from dbscSNV. (plugin details) 0 -
distance Integer Change the distance to transcript for which VEP assigns upstream and downstream consequences 5000 -
domains Boolean Include names of overlapping protein domains 0 -
failed Boolean When checking for co-located variants, by default variants flagged as failed by Ensembl's QC pipeline will be excluded. Set this flag to 1 to include such variants 0 -
hgvs Boolean Include HGVS nomenclature based on Ensembl stable identifiers 0 -
mane Boolean Include MANE Select annotations (GRCh38 only) 0 -
merged Boolean Use merged Ensembl and RefSeq transcript set to report consequences (human only) 0 -
miRNA Boolean Determines where in the secondary structure of a miRNA a variant falls (plugin details) 0 -
minimal Boolean Convert alleles to their most minimal representation before consequence calculation i.e. sequence that is identical between each pair of reference and alternate alleles is trimmed off from both ends, with coordinates adjusted accordingly. Note this may lead to discrepancies between input coordinates and coordinates reported by VEP relative to transcript sequences 0 -
mutfunc Boolean Predicts destabilization effect of protein structure, interaction, regulatory region etc. caused by a variant as reported by mutfunc database. (plugin details) 0 -
numbers Boolean Include affected exon and intron positions within the transcript 0 -
protein Boolean Include Ensembl protein identifiers 0 -
refseq Boolean Use RefSeq transcript set to report consequences (human only) 0 -
shift_3prime Boolean Shift transcript-overlapping variants as far as possible in the 3' direction before providing consequences 0 -
shift_genomic Boolean Shift all variants as far as possible in the 3' direction before providing consequences 0 -
transcript_id String Filter results by Transcript ID Not Used -
transcript_version Boolean Add version numbers to Ensembl transcript identifiers 0 -
tsl Boolean Include transcript support level (TSL) annotation 0 -
uniprot Boolean Include best match accessions for translated protein products from three UniProt-related databases (SWISSPROT, TREMBL and UniParc) 0 -
variant_class Boolean Output the Sequence Ontology variant class for the input variant 0 -
vcf_string Boolean Include alleles in VCF format 0 -
xref_refseq Boolean Include aligned RefSeq mRNA identifiers for transcript. NB: theRefSeq and Ensembl transcripts aligned in this way MAY NOT, AND FREQUENTLY WILL NOT, match exactly in sequence, exon structure and protein product 0 -

Example Requests

/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});

die "Failed!\n" unless $response->{success};


use JSON;
use Data::Dumper;
if(length $response->{content}) {
  my $hash = decode_json($response->{content});
  local $Data::Dumper::Terse = 1;
  local $Data::Dumper::Indent = 1;
  print Dumper $hash;
  print "\n";
}


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print repr(decoded)


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))


require 'net/http'
require 'uri'

server='https://jan2020.rest.ensembl.org'
path = '/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?'

url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)

request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})

response = http.request(request)

if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end


require 'rubygems'
require 'json'
require 'yaml'

result = JSON.parse(response.body)
puts YAML::dump(result)


import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;


public class EnsemblRest {

  public static void main(String[] args) throws Exception {
    String server = "https://jan2020.rest.ensembl.org";
    String ext = "/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "application/json");
    

    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();

    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }

    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }

    System.out.println(output);
  }
}


library(httr)
library(jsonlite)
library(xml2)

server <- "https://jan2020.rest.ensembl.org"
ext <- "/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))



curl 'https://jan2020.rest.ensembl.org/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/vep/human/hgvs/ENSP00000401091.1:p.Tyr124Cys?'  -O -

/vep/human/hgvs/ENST00000366667:c.803C>T?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/vep/human/hgvs/ENST00000366667:c.803C%3ET?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});

die "Failed!\n" unless $response->{success};


use JSON;
use Data::Dumper;
if(length $response->{content}) {
  my $hash = decode_json($response->{content});
  local $Data::Dumper::Terse = 1;
  local $Data::Dumper::Indent = 1;
  print Dumper $hash;
  print "\n";
}


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/ENST00000366667:c.803C>T?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print repr(decoded)


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/ENST00000366667:c.803C>T?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))


require 'net/http'
require 'uri'

server='https://jan2020.rest.ensembl.org'
path = '/vep/human/hgvs/ENST00000366667:c.803C%3ET?'

url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)

request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})

response = http.request(request)

if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end


require 'rubygems'
require 'json'
require 'yaml'

result = JSON.parse(response.body)
puts YAML::dump(result)


import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;


public class EnsemblRest {

  public static void main(String[] args) throws Exception {
    String server = "https://jan2020.rest.ensembl.org";
    String ext = "/vep/human/hgvs/ENST00000366667:c.803C%3ET?";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "application/json");
    

    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();

    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }

    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }

    System.out.println(output);
  }
}


library(httr)
library(jsonlite)
library(xml2)

server <- "https://jan2020.rest.ensembl.org"
ext <- "/vep/human/hgvs/ENST00000366667:c.803C>T?"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))



curl 'https://jan2020.rest.ensembl.org/vep/human/hgvs/ENST00000366667:c.803C%3ET?' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/vep/human/hgvs/ENST00000366667:c.803C>T?'  -O -

/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});

die "Failed!\n" unless $response->{success};


use JSON;
use Data::Dumper;
if(length $response->{content}) {
  my $hash = decode_json($response->{content});
  local $Data::Dumper::Terse = 1;
  local $Data::Dumper::Indent = 1;
  print Dumper $hash;
  print "\n";
}


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print repr(decoded)


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))


require 'net/http'
require 'uri'

server='https://jan2020.rest.ensembl.org'
path = '/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?'

url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)

request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})

response = http.request(request)

if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end


require 'rubygems'
require 'json'
require 'yaml'

result = JSON.parse(response.body)
puts YAML::dump(result)


import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;


public class EnsemblRest {

  public static void main(String[] args) throws Exception {
    String server = "https://jan2020.rest.ensembl.org";
    String ext = "/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "application/json");
    

    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();

    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }

    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }

    System.out.println(output);
  }
}


library(httr)
library(jsonlite)
library(xml2)

server <- "https://jan2020.rest.ensembl.org"
ext <- "/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))



curl 'https://jan2020.rest.ensembl.org/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/vep/human/hgvs/ENST00000003084:c.1431_1433delTTC?'  -O -

/vep/human/hgvs/9:g.22125504G>C?content-type=application/json


use strict;
use warnings;

use HTTP::Tiny;

my $http = HTTP::Tiny->new();

my $server = 'https://jan2020.rest.ensembl.org';
my $ext = '/vep/human/hgvs/9:g.22125504G%3EC?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});

die "Failed!\n" unless $response->{success};


use JSON;
use Data::Dumper;
if(length $response->{content}) {
  my $hash = decode_json($response->{content});
  local $Data::Dumper::Terse = 1;
  local $Data::Dumper::Indent = 1;
  print Dumper $hash;
  print "\n";
}


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/9:g.22125504G>C?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print repr(decoded)


import requests, sys

server = "https://jan2020.rest.ensembl.org"
ext = "/vep/human/hgvs/9:g.22125504G>C?"

r = requests.get(server+ext, headers={ "Content-Type" : "application/json"})

if not r.ok:
  r.raise_for_status()
  sys.exit()

decoded = r.json()
print(repr(decoded))


require 'net/http'
require 'uri'

server='https://jan2020.rest.ensembl.org'
path = '/vep/human/hgvs/9:g.22125504G%3EC?'

url = URI.parse(server)
http = Net::HTTP.new(url.host, url.port)

request = Net::HTTP::Get.new(path, {'Content-Type' => 'application/json'})

response = http.request(request)

if response.code != "200"
  puts "Invalid response: #{response.code}"
  puts response.body
  exit
end


require 'rubygems'
require 'json'
require 'yaml'

result = JSON.parse(response.body)
puts YAML::dump(result)


import java.net.URL;
import java.net.URLConnection;
import java.net.HttpURLConnection;
import java.io.BufferedReader;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.IOException;
import java.io.Reader;


public class EnsemblRest {

  public static void main(String[] args) throws Exception {
    String server = "https://jan2020.rest.ensembl.org";
    String ext = "/vep/human/hgvs/9:g.22125504G%3EC?";
    URL url = new URL(server + ext);

    URLConnection connection = url.openConnection();
    HttpURLConnection httpConnection = (HttpURLConnection)connection;
    
    httpConnection.setRequestProperty("Content-Type", "application/json");
    

    InputStream response = connection.getInputStream();
    int responseCode = httpConnection.getResponseCode();

    if(responseCode != 200) {
      throw new RuntimeException("Response code was not 200. Detected response was "+responseCode);
    }

    String output;
    Reader reader = null;
    try {
      reader = new BufferedReader(new InputStreamReader(response, "UTF-8"));
      StringBuilder builder = new StringBuilder();
      char[] buffer = new char[8192];
      int read;
      while ((read = reader.read(buffer, 0, buffer.length)) > 0) {
        builder.append(buffer, 0, read);
      }
      output = builder.toString();
    } 
    finally {
        if (reader != null) try {
          reader.close(); 
        } catch (IOException logOrIgnore) {
          logOrIgnore.printStackTrace();
        }
    }

    System.out.println(output);
  }
}


library(httr)
library(jsonlite)
library(xml2)

server <- "https://jan2020.rest.ensembl.org"
ext <- "/vep/human/hgvs/9:g.22125504G>C?"

r <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(r)

# use this if you get a simple nested list back, otherwise inspect its structure
# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))



curl 'https://jan2020.rest.ensembl.org/vep/human/hgvs/9:g.22125504G%3EC?' -H 'Content-type:application/json'


wget -q --header='Content-type:application/json' 'https://jan2020.rest.ensembl.org/vep/human/hgvs/9:g.22125504G>C?'  -O -

Resource Information

MethodsGET
Response formatsjson
xml
jsonp