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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: 9-131523012-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=131523012&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 131523012,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000402686.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2084G>A",
"hgvs_p": "p.Arg695His",
"transcript": "NM_001077365.2",
"protein_id": "NP_001070833.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 725,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 2270,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": "ENST00000402686.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2084G>A",
"hgvs_p": "p.Arg695His",
"transcript": "ENST00000402686.8",
"protein_id": "ENSP00000385797.4",
"transcript_support_level": 1,
"aa_start": 695,
"aa_end": null,
"aa_length": 725,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 2270,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": "NM_001077365.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2150G>A",
"hgvs_p": "p.Arg717His",
"transcript": "ENST00000372228.9",
"protein_id": "ENSP00000361302.3",
"transcript_support_level": 1,
"aa_start": 717,
"aa_end": null,
"aa_length": 747,
"cds_start": 2150,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 2465,
"cdna_end": null,
"cdna_length": 3252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2141G>A",
"hgvs_p": "p.Arg714His",
"transcript": "ENST00000423007.6",
"protein_id": "ENSP00000404119.2",
"transcript_support_level": 1,
"aa_start": 714,
"aa_end": null,
"aa_length": 744,
"cds_start": 2141,
"cds_end": null,
"cds_length": 2235,
"cdna_start": 2141,
"cdna_end": null,
"cdna_length": 2235,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2150G>A",
"hgvs_p": "p.Arg717His",
"transcript": "NM_001353193.2",
"protein_id": "NP_001340122.2",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 747,
"cds_start": 2150,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 2576,
"cdna_end": null,
"cdna_length": 3363,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2150G>A",
"hgvs_p": "p.Arg717His",
"transcript": "NM_007171.4",
"protein_id": "NP_009102.4",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 747,
"cds_start": 2150,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 2336,
"cdna_end": null,
"cdna_length": 3123,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2084G>A",
"hgvs_p": "p.Arg695His",
"transcript": "NM_001136113.2",
"protein_id": "NP_001129585.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 725,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 2510,
"cdna_end": null,
"cdna_length": 3297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2084G>A",
"hgvs_p": "p.Arg695His",
"transcript": "ENST00000676640.1",
"protein_id": "ENSP00000503281.1",
"transcript_support_level": null,
"aa_start": 695,
"aa_end": null,
"aa_length": 725,
"cds_start": 2084,
"cds_end": null,
"cds_length": 2178,
"cdna_start": 2522,
"cdna_end": null,
"cdna_length": 3309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.2072G>A",
"hgvs_p": "p.Arg691His",
"transcript": "NM_001374689.1",
"protein_id": "NP_001361618.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 721,
"cds_start": 2072,
"cds_end": null,
"cds_length": 2166,
"cdna_start": 2268,
"cdna_end": null,
"cdna_length": 3055,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1994G>A",
"hgvs_p": "p.Arg665His",
"transcript": "NM_001353196.2",
"protein_id": "NP_001340125.1",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 695,
"cds_start": 1994,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2180,
"cdna_end": null,
"cdna_length": 2967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1994G>A",
"hgvs_p": "p.Arg665His",
"transcript": "ENST00000678303.1",
"protein_id": "ENSP00000503696.1",
"transcript_support_level": null,
"aa_start": 665,
"aa_end": null,
"aa_length": 695,
"cds_start": 1994,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 2150,
"cdna_end": null,
"cdna_length": 2573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1988G>A",
"hgvs_p": "p.Arg663His",
"transcript": "NM_001353197.2",
"protein_id": "NP_001340126.2",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 693,
"cds_start": 1988,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 2184,
"cdna_end": null,
"cdna_length": 2971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1988G>A",
"hgvs_p": "p.Arg663His",
"transcript": "NM_001353198.2",
"protein_id": "NP_001340127.2",
"transcript_support_level": null,
"aa_start": 663,
"aa_end": null,
"aa_length": 693,
"cds_start": 1988,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 2885,
"cdna_end": null,
"cdna_length": 3672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1922G>A",
"hgvs_p": "p.Arg641His",
"transcript": "NM_001077366.2",
"protein_id": "NP_001070834.1",
"transcript_support_level": null,
"aa_start": 641,
"aa_end": null,
"aa_length": 671,
"cds_start": 1922,
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"cds_length": 2016,
"cdna_start": 2118,
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"cdna_length": 2905,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1922G>A",
"hgvs_p": "p.Arg641His",
"transcript": "NM_001353194.2",
"protein_id": "NP_001340123.1",
"transcript_support_level": null,
"aa_start": 641,
"aa_end": null,
"aa_length": 671,
"cds_start": 1922,
"cds_end": null,
"cds_length": 2016,
"cdna_start": 2358,
"cdna_end": null,
"cdna_length": 3145,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1922G>A",
"hgvs_p": "p.Arg641His",
"transcript": "ENST00000341012.13",
"protein_id": "ENSP00000343034.7",
"transcript_support_level": 2,
"aa_start": 641,
"aa_end": null,
"aa_length": 671,
"cds_start": 1922,
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"cdna_start": 2141,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1865G>A",
"hgvs_p": "p.Arg622His",
"transcript": "NM_001374690.1",
"protein_id": "NP_001361619.1",
"transcript_support_level": null,
"aa_start": 622,
"aa_end": null,
"aa_length": 652,
"cds_start": 1865,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 2051,
"cdna_end": null,
"cdna_length": 2838,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1799G>A",
"hgvs_p": "p.Arg600His",
"transcript": "NM_001353199.2",
"protein_id": "NP_001340128.2",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 630,
"cds_start": 1799,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 2077,
"cdna_end": null,
"cdna_length": 2864,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1733G>A",
"hgvs_p": "p.Arg578His",
"transcript": "NM_001136114.2",
"protein_id": "NP_001129586.1",
"transcript_support_level": null,
"aa_start": 578,
"aa_end": null,
"aa_length": 608,
"cds_start": 1733,
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"cdna_start": 2011,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1733G>A",
"hgvs_p": "p.Arg578His",
"transcript": "NM_001353195.2",
"protein_id": "NP_001340124.1",
"transcript_support_level": null,
"aa_start": 578,
"aa_end": null,
"aa_length": 608,
"cds_start": 1733,
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"feature": null
},
{
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"aa_alt": "H",
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"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1733G>A",
"hgvs_p": "p.Arg578His",
"transcript": "NM_001374691.1",
"protein_id": "NP_001361620.1",
"transcript_support_level": null,
"aa_start": 578,
"aa_end": null,
"aa_length": 608,
"cds_start": 1733,
"cds_end": null,
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"cdna_start": 2200,
"cdna_end": null,
"cdna_length": 2987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "c.1733G>A",
"hgvs_p": "p.Arg578His",
"transcript": "NM_001374692.1",
"protein_id": "NP_001361621.1",
"transcript_support_level": null,
"aa_start": 578,
"aa_end": null,
"aa_length": 608,
"cds_start": 1733,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 2112,
"cdna_end": null,
"cdna_length": 2899,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
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"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"hgvs_c": "n.*840G>A",
"hgvs_p": null,
"transcript": "ENST00000679111.1",
"protein_id": "ENSP00000504257.1",
"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": 3164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "POMT1",
"gene_hgnc_id": 9202,
"dbsnp": "rs373402995",
"frequency_reference_population": 0.000055291315,
"hom_count_reference_population": 0,
"allele_count_reference_population": 89,
"gnomad_exomes_af": 0.0000590069,
"gnomad_genomes_af": 0.0000197109,
"gnomad_exomes_ac": 86,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6817287802696228,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.566,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0877,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.66,
"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": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000402686.8",
"gene_symbol": "POMT1",
"hgnc_id": 9202,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2084G>A",
"hgvs_p": "p.Arg695His"
}
],
"clinvar_disease": " type B1,Autosomal recessive limb-girdle muscular dystrophy type 2K,Inborn genetic diseases,Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability),Walker-Warburg congenital muscular dystrophy,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Autosomal recessive limb-girdle muscular dystrophy type 2K;Walker-Warburg congenital muscular dystrophy;Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}