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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: 4-54731930-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=54731930&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 54731930,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000288135.6",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2293G>T",
"hgvs_p": "p.Asp765Tyr",
"transcript": "NM_000222.3",
"protein_id": "NP_000213.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 976,
"cds_start": 2293,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2351,
"cdna_end": null,
"cdna_length": 5147,
"mane_select": "ENST00000288135.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2293G>T",
"hgvs_p": "p.Asp765Tyr",
"transcript": "ENST00000288135.6",
"protein_id": "ENSP00000288135.6",
"transcript_support_level": 1,
"aa_start": 765,
"aa_end": null,
"aa_length": 976,
"cds_start": 2293,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2351,
"cdna_end": null,
"cdna_length": 5147,
"mane_select": "NM_000222.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2281G>T",
"hgvs_p": "p.Asp761Tyr",
"transcript": "ENST00000412167.7",
"protein_id": "ENSP00000390987.3",
"transcript_support_level": 1,
"aa_start": 761,
"aa_end": null,
"aa_length": 972,
"cds_start": 2281,
"cds_end": null,
"cds_length": 2919,
"cdna_start": 2373,
"cdna_end": null,
"cdna_length": 5126,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2296G>T",
"hgvs_p": "p.Asp766Tyr",
"transcript": "NM_001385284.1",
"protein_id": "NP_001372213.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 977,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2934,
"cdna_start": 2354,
"cdna_end": null,
"cdna_length": 5150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2296G>T",
"hgvs_p": "p.Asp766Tyr",
"transcript": "ENST00000687109.1",
"protein_id": "ENSP00000509371.1",
"transcript_support_level": null,
"aa_start": 766,
"aa_end": null,
"aa_length": 977,
"cds_start": 2296,
"cds_end": null,
"cds_length": 2934,
"cdna_start": 2398,
"cdna_end": null,
"cdna_length": 5249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2293G>T",
"hgvs_p": "p.Asp765Tyr",
"transcript": "NM_001385290.1",
"protein_id": "NP_001372219.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 976,
"cds_start": 2293,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2351,
"cdna_end": null,
"cdna_length": 5147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2293G>T",
"hgvs_p": "p.Asp765Tyr",
"transcript": "ENST00000689832.1",
"protein_id": "ENSP00000509084.1",
"transcript_support_level": null,
"aa_start": 765,
"aa_end": null,
"aa_length": 976,
"cds_start": 2293,
"cds_end": null,
"cds_length": 2931,
"cdna_start": 2341,
"cdna_end": null,
"cdna_length": 5098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2290G>T",
"hgvs_p": "p.Asp764Tyr",
"transcript": "NM_001385285.1",
"protein_id": "NP_001372214.1",
"transcript_support_level": null,
"aa_start": 764,
"aa_end": null,
"aa_length": 975,
"cds_start": 2290,
"cds_end": null,
"cds_length": 2928,
"cdna_start": 2348,
"cdna_end": null,
"cdna_length": 5144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2290G>T",
"hgvs_p": "p.Asp764Tyr",
"transcript": "ENST00000692783.1",
"protein_id": "ENSP00000508733.1",
"transcript_support_level": null,
"aa_start": 764,
"aa_end": null,
"aa_length": 975,
"cds_start": 2290,
"cds_end": null,
"cds_length": 2928,
"cdna_start": 2382,
"cdna_end": null,
"cdna_length": 5230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2284G>T",
"hgvs_p": "p.Asp762Tyr",
"transcript": "NM_001385288.1",
"protein_id": "NP_001372217.1",
"transcript_support_level": null,
"aa_start": 762,
"aa_end": null,
"aa_length": 973,
"cds_start": 2284,
"cds_end": null,
"cds_length": 2922,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 5138,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2284G>T",
"hgvs_p": "p.Asp762Tyr",
"transcript": "ENST00000690543.1",
"protein_id": "ENSP00000508831.1",
"transcript_support_level": null,
"aa_start": 762,
"aa_end": null,
"aa_length": 973,
"cds_start": 2284,
"cds_end": null,
"cds_length": 2922,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 5121,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2281G>T",
"hgvs_p": "p.Asp761Tyr",
"transcript": "NM_001093772.2",
"protein_id": "NP_001087241.1",
"transcript_support_level": null,
"aa_start": 761,
"aa_end": null,
"aa_length": 972,
"cds_start": 2281,
"cds_end": null,
"cds_length": 2919,
"cdna_start": 2339,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2281G>T",
"hgvs_p": "p.Asp761Tyr",
"transcript": "NM_001385292.1",
"protein_id": "NP_001372221.1",
"transcript_support_level": null,
"aa_start": 761,
"aa_end": null,
"aa_length": 972,
"cds_start": 2281,
"cds_end": null,
"cds_length": 2919,
"cdna_start": 2339,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2281G>T",
"hgvs_p": "p.Asp761Tyr",
"transcript": "ENST00000687295.1",
"protein_id": "ENSP00000509450.1",
"transcript_support_level": null,
"aa_start": 761,
"aa_end": null,
"aa_length": 972,
"cds_start": 2281,
"cds_end": null,
"cds_length": 2919,
"cdna_start": 2407,
"cdna_end": null,
"cdna_length": 5271,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2278G>T",
"hgvs_p": "p.Asp760Tyr",
"transcript": "NM_001385286.1",
"protein_id": "NP_001372215.1",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 971,
"cds_start": 2278,
"cds_end": null,
"cds_length": 2916,
"cdna_start": 2336,
"cdna_end": null,
"cdna_length": 5132,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2278G>T",
"hgvs_p": "p.Asp760Tyr",
"transcript": "ENST00000686011.1",
"protein_id": "ENSP00000509704.1",
"transcript_support_level": null,
"aa_start": 760,
"aa_end": null,
"aa_length": 971,
"cds_start": 2278,
"cds_end": null,
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"cdna_start": 2351,
"cdna_end": null,
"cdna_length": 5135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.2281G>T",
"hgvs_p": "p.Asp761Tyr",
"transcript": "ENST00000687246.1",
"protein_id": "ENSP00000509114.1",
"transcript_support_level": null,
"aa_start": 761,
"aa_end": null,
"aa_length": 931,
"cds_start": 2281,
"cds_end": null,
"cds_length": 2796,
"cdna_start": 2349,
"cdna_end": null,
"cdna_length": 5022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "c.1783G>T",
"hgvs_p": "p.Asp595Tyr",
"transcript": "ENST00000689994.1",
"protein_id": "ENSP00000509156.1",
"transcript_support_level": null,
"aa_start": 595,
"aa_end": null,
"aa_length": 806,
"cds_start": 1783,
"cds_end": null,
"cds_length": 2421,
"cdna_start": 2315,
"cdna_end": null,
"cdna_length": 5091,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "n.346G>T",
"hgvs_p": null,
"transcript": "ENST00000512959.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 746,
"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": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "n.2371G>T",
"hgvs_p": null,
"transcript": "ENST00000685269.1",
"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,
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"cdna_length": 5116,
"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": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "n.2705G>T",
"hgvs_p": null,
"transcript": "ENST00000687208.1",
"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": 5483,
"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": 16,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "n.2451G>T",
"hgvs_p": null,
"transcript": "ENST00000687265.1",
"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": 5226,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"hgvs_c": "n.90G>T",
"hgvs_p": null,
"transcript": "ENST00000688060.1",
"protein_id": null,
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"aa_start": null,
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},
{
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},
{
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},
{
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},
{
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],
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}
],
"gene_symbol": "KIT",
"gene_hgnc_id": 6342,
"dbsnp": "rs760112920",
"frequency_reference_population": 0.0000061975684,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000273681,
"gnomad_genomes_af": 0.0000394784,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.897507905960083,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.701,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5644,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.33,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.976,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP2,PP3_Moderate,BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 5,
"pathogenic_score": 3,
"criteria": [
"PP2",
"PP3_Moderate",
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000288135.6",
"gene_symbol": "KIT",
"hgnc_id": 6342,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2293G>T",
"hgvs_p": "p.Asp765Tyr"
}
],
"clinvar_disease": "Gastrointestinal stromal tumor,Hereditary cancer-predisposing syndrome,KIT-related disorder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Gastrointestinal stromal tumor|KIT-related disorder|Hereditary cancer-predisposing syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}