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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 10-87952250-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=87952250&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 87952250,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000371953.8",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Arg",
"transcript": "NM_000314.8",
"protein_id": "NP_000305.3",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 403,
"cds_start": 625,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1470,
"cdna_end": null,
"cdna_length": 8515,
"mane_select": "ENST00000371953.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Arg",
"transcript": "ENST00000371953.8",
"protein_id": "ENSP00000361021.3",
"transcript_support_level": 1,
"aa_start": 209,
"aa_end": null,
"aa_length": 403,
"cds_start": 625,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1470,
"cdna_end": null,
"cdna_length": 8515,
"mane_select": "NM_000314.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Gly382Arg",
"transcript": "NM_001304717.5",
"protein_id": "NP_001291646.4",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 576,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1731,
"cdna_start": 1469,
"cdna_end": null,
"cdna_length": 8514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.1144G>A",
"hgvs_p": "p.Gly382Arg",
"transcript": "ENST00000693560.1",
"protein_id": "ENSP00000509861.1",
"transcript_support_level": null,
"aa_start": 382,
"aa_end": null,
"aa_length": 576,
"cds_start": 1144,
"cds_end": null,
"cds_length": 1731,
"cdna_start": 1656,
"cdna_end": null,
"cdna_length": 8701,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Arg",
"transcript": "ENST00000700029.2",
"protein_id": "ENSP00000514759.2",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 434,
"cds_start": 625,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 1470,
"cdna_end": null,
"cdna_length": 3563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.718G>A",
"hgvs_p": "p.Gly240Arg",
"transcript": "ENST00000713839.1",
"protein_id": "ENSP00000519144.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 434,
"cds_start": 718,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 1555,
"cdna_end": null,
"cdna_length": 3555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Arg",
"transcript": "ENST00000688308.1",
"protein_id": "ENSP00000508752.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 403,
"cds_start": 625,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 1117,
"cdna_end": null,
"cdna_length": 3117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.580G>A",
"hgvs_p": "p.Gly194Arg",
"transcript": "ENST00000700021.1",
"protein_id": "ENSP00000514757.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 388,
"cds_start": 580,
"cds_end": null,
"cds_length": 1167,
"cdna_start": 1255,
"cdna_end": null,
"cdna_length": 3255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Arg",
"transcript": "ENST00000472832.3",
"protein_id": "ENSP00000483066.2",
"transcript_support_level": 2,
"aa_start": 209,
"aa_end": null,
"aa_length": 344,
"cds_start": 625,
"cds_end": null,
"cds_length": 1035,
"cdna_start": 766,
"cdna_end": null,
"cdna_length": 1358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "c.34G>A",
"hgvs_p": "p.Gly12Arg",
"transcript": "NM_001304718.2",
"protein_id": "NP_001291647.1",
"transcript_support_level": null,
"aa_start": 12,
"aa_end": null,
"aa_length": 206,
"cds_start": 34,
"cds_end": null,
"cds_length": 621,
"cdna_start": 1584,
"cdna_end": null,
"cdna_length": 8629,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*211G>A",
"hgvs_p": null,
"transcript": "ENST00000686459.1",
"protein_id": "ENSP00000508909.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.1360G>A",
"hgvs_p": null,
"transcript": "ENST00000688158.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8405,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*455G>A",
"hgvs_p": null,
"transcript": "ENST00000688922.2",
"protein_id": "ENSP00000508742.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.1783G>A",
"hgvs_p": null,
"transcript": "ENST00000700023.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.2017G>A",
"hgvs_p": null,
"transcript": "ENST00000700024.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.1394G>A",
"hgvs_p": null,
"transcript": "ENST00000700025.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3127,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*660G>A",
"hgvs_p": null,
"transcript": "ENST00000706955.1",
"protein_id": "ENSP00000516675.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.625G>A",
"hgvs_p": null,
"transcript": "ENST00000710265.1",
"protein_id": "ENSP00000518161.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*538G>A",
"hgvs_p": null,
"transcript": "ENST00000713837.1",
"protein_id": "ENSP00000519142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*211G>A",
"hgvs_p": null,
"transcript": "ENST00000686459.1",
"protein_id": "ENSP00000508909.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*455G>A",
"hgvs_p": null,
"transcript": "ENST00000688922.2",
"protein_id": "ENSP00000508742.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2818,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*660G>A",
"hgvs_p": null,
"transcript": "ENST00000706955.1",
"protein_id": "ENSP00000516675.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8685,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.*538G>A",
"hgvs_p": null,
"transcript": "ENST00000713837.1",
"protein_id": "ENSP00000519142.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"hgvs_c": "n.493-5603G>A",
"hgvs_p": null,
"transcript": "ENST00000700022.1",
"protein_id": "ENSP00000514758.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2794,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTEN",
"gene_hgnc_id": 9588,
"dbsnp": "rs765433422",
"frequency_reference_population": 0.0000065754866,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0.00000205407,
"gnomad_genomes_af": 0.00000657549,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8231893181800842,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.683,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9875,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.487,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000371953.8",
"gene_symbol": "PTEN",
"hgnc_id": 9588,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Gly209Arg"
}
],
"clinvar_disease": "Hereditary cancer-predisposing syndrome,PTEN hamartoma tumor syndrome",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:4 LB:1",
"phenotype_combined": "Hereditary cancer-predisposing syndrome|PTEN hamartoma tumor syndrome",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}