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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: 19-17337613-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=17337613&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 17337613,
"ref": "T",
"alt": "C",
"effect": "start_lost",
"transcript": "NM_133644.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_032620.4",
"protein_id": "NP_116009.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 492,
"cds_start": 2,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 61,
"cdna_end": null,
"cdna_length": 2566,
"mane_select": "ENST00000324894.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032620.4"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000324894.13",
"protein_id": "ENSP00000313818.7",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 492,
"cds_start": 2,
"cds_end": null,
"cds_length": 1479,
"cdna_start": 61,
"cdna_end": null,
"cdna_length": 2566,
"mane_select": "NM_032620.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324894.13"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000600625.5",
"protein_id": "ENSP00000473150.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 471,
"cds_start": 2,
"cds_end": null,
"cds_length": 1416,
"cdna_start": 59,
"cdna_end": null,
"cdna_length": 2493,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600625.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000600610.5",
"protein_id": "ENSP00000469008.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1105,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000600610.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_133644.4",
"protein_id": "NP_598399.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 524,
"cds_start": 2,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 61,
"cdna_end": null,
"cdna_length": 2662,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_133644.4"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000358792.11",
"protein_id": "ENSP00000351644.6",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 524,
"cds_start": 2,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 59,
"cdna_end": null,
"cdna_length": 1951,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358792.11"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000934088.1",
"protein_id": "ENSP00000604147.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 473,
"cds_start": 2,
"cds_end": null,
"cds_length": 1422,
"cdna_start": 43,
"cdna_end": null,
"cdna_length": 2487,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934088.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001128855.3",
"protein_id": "NP_001122327.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 471,
"cds_start": 2,
"cds_end": null,
"cds_length": 1416,
"cdna_start": 61,
"cdna_end": null,
"cdna_length": 2503,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128855.3"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000934087.1",
"protein_id": "ENSP00000604146.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 444,
"cds_start": 2,
"cds_end": null,
"cds_length": 1335,
"cdna_start": 69,
"cdna_end": null,
"cdna_length": 2434,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934087.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.120-395T>C",
"hgvs_p": null,
"transcript": "NM_001195422.1",
"protein_id": "NP_001182351.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 514,
"cds_start": null,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2595,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001195422.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.120-395T>C",
"hgvs_p": null,
"transcript": "ENST00000361619.9",
"protein_id": "ENSP00000354598.4",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 514,
"cds_start": null,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1894,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361619.9"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000594018.5",
"protein_id": "ENSP00000471421.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 934,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000594018.5"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.28T>C",
"hgvs_p": null,
"transcript": "ENST00000596001.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1072,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000596001.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.55T>C",
"hgvs_p": null,
"transcript": "ENST00000596166.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1024,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000596166.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000598493.5",
"protein_id": "ENSP00000472156.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 808,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000598493.5"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.97T>C",
"hgvs_p": null,
"transcript": "ENST00000599429.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 592,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000599429.5"
},
{
"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": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000602165.1",
"protein_id": "ENSP00000470109.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 617,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000602165.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.18+37T>C",
"hgvs_p": null,
"transcript": "ENST00000593297.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 555,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000593297.5"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.467-395T>C",
"hgvs_p": null,
"transcript": "ENST00000594345.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1004,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000594345.5"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.431-261T>C",
"hgvs_p": null,
"transcript": "ENST00000595951.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 532,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000595951.1"
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.297+344T>C",
"hgvs_p": null,
"transcript": "ENST00000596218.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 897,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000596218.5"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.163-395T>C",
"hgvs_p": null,
"transcript": "ENST00000596941.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 678,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000596941.5"
},
{
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
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{
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{
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"biotype": "nonsense_mediated_decay",
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{
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],
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"biotype": "retained_intron",
"feature": "ENST00000601261.5"
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{
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{
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],
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"exon_count": 2,
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"gene_symbol": "GTPBP3",
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{
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],
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"gene_symbol": "ENSG00000307319",
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"biotype": "pseudogene",
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],
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"dbsnp": "rs1019249439",
"frequency_reference_population": 0.0000025611912,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000256119,
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"gnomad_exomes_ac": 3,
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"gnomad_exomes_homalt": 0,
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"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9735910892486572,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.294,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.236,
"phylop100way_prediction": "Benign",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_133644.4",
"gene_symbol": "GTPBP3",
"hgnc_id": 14880,
"effects": [
"start_lost"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?"
},
{
"score": 8,
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"pathogenic_score": 8,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000825048.1",
"gene_symbol": "ENSG00000307319",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.162+303A>G",
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}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}