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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: 2-63492856-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=63492856&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 63492856,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000272321.12",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "NM_015910.7",
"protein_id": "NP_056994.3",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 746,
"cds_start": 160,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 4894,
"mane_select": "ENST00000272321.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "ENST00000272321.12",
"protein_id": "ENSP00000272321.7",
"transcript_support_level": 1,
"aa_start": 54,
"aa_end": null,
"aa_length": 746,
"cds_start": 160,
"cds_end": null,
"cds_length": 2241,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 4894,
"mane_select": "NM_015910.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "ENST00000409562.7",
"protein_id": "ENSP00000387222.3",
"transcript_support_level": 1,
"aa_start": 54,
"aa_end": null,
"aa_length": 618,
"cds_start": 160,
"cds_end": null,
"cds_length": 1857,
"cdna_start": 407,
"cdna_end": null,
"cdna_length": 3544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "n.407G>A",
"hgvs_p": null,
"transcript": "ENST00000409835.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 2277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.88G>A",
"hgvs_p": "p.Asp30Asn",
"transcript": "NM_001354044.2",
"protein_id": "NP_001340973.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 722,
"cds_start": 88,
"cds_end": null,
"cds_length": 2169,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 5146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "NM_001354045.2",
"protein_id": "NP_001340974.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 649,
"cds_start": 160,
"cds_end": null,
"cds_length": 1950,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 2337,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "ENST00000431065.1",
"protein_id": "ENSP00000396226.1",
"transcript_support_level": 4,
"aa_start": 54,
"aa_end": null,
"aa_length": 83,
"cds_start": 160,
"cds_end": null,
"cds_length": 254,
"cdna_start": 688,
"cdna_end": null,
"cdna_length": 782,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "XM_005264348.5",
"protein_id": "XP_005264405.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 781,
"cds_start": 160,
"cds_end": null,
"cds_length": 2346,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 4814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.88G>A",
"hgvs_p": "p.Asp30Asn",
"transcript": "XM_011532881.4",
"protein_id": "XP_011531183.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 757,
"cds_start": 88,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 618,
"cdna_end": null,
"cdna_length": 5066,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.88G>A",
"hgvs_p": "p.Asp30Asn",
"transcript": "XM_047444626.1",
"protein_id": "XP_047300582.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 757,
"cds_start": 88,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 5774,
"cdna_end": null,
"cdna_length": 10222,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.88G>A",
"hgvs_p": "p.Asp30Asn",
"transcript": "XM_047444627.1",
"protein_id": "XP_047300583.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 757,
"cds_start": 88,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 1387,
"cdna_end": null,
"cdna_length": 5835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.88G>A",
"hgvs_p": "p.Asp30Asn",
"transcript": "XM_047444628.1",
"protein_id": "XP_047300584.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 757,
"cds_start": 88,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 5073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.88G>A",
"hgvs_p": "p.Asp30Asn",
"transcript": "XM_047444629.1",
"protein_id": "XP_047300585.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 757,
"cds_start": 88,
"cds_end": null,
"cds_length": 2274,
"cdna_start": 1301,
"cdna_end": null,
"cdna_length": 5749,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.61G>A",
"hgvs_p": "p.Asp21Asn",
"transcript": "XM_047444630.1",
"protein_id": "XP_047300586.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 748,
"cds_start": 61,
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"cds_length": 2247,
"cdna_start": 1496,
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"cdna_length": 5944,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.88G>A",
"hgvs_p": "p.Asp30Asn",
"transcript": "XM_047444631.1",
"protein_id": "XP_047300587.1",
"transcript_support_level": null,
"aa_start": 30,
"aa_end": null,
"aa_length": 722,
"cds_start": 88,
"cds_end": null,
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"cdna_start": 1301,
"cdna_end": null,
"cdna_length": 5829,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "XM_011532884.4",
"protein_id": "XP_011531186.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 652,
"cds_start": 160,
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"cds_length": 1959,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 11693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "XM_047444632.1",
"protein_id": "XP_047300588.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 648,
"cds_start": 160,
"cds_end": null,
"cds_length": 1947,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 2280,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "XM_011532887.4",
"protein_id": "XP_011531189.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 642,
"cds_start": 160,
"cds_end": null,
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"cdna_start": 366,
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"mane_select": null,
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"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "XM_017004253.3",
"protein_id": "XP_016859742.1",
"transcript_support_level": null,
"aa_start": 54,
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"cds_start": 160,
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"cdna_start": 366,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "XM_011532890.4",
"protein_id": "XP_011531192.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
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"cds_start": 160,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn",
"transcript": "XM_047444634.1",
"protein_id": "XP_047300590.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 542,
"cds_start": 160,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 366,
"cdna_end": null,
"cdna_length": 1949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WDPCP",
"gene_hgnc_id": 28027,
"hgvs_c": "n.*271G>A",
"hgvs_p": null,
"transcript": "ENST00000417238.5",
"protein_id": "ENSP00000411429.1",
"transcript_support_level": 2,
"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": 2883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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}
],
"gene_symbol": "WDPCP",
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"dbsnp": "rs200322968",
"frequency_reference_population": 0.00023374772,
"hom_count_reference_population": 0,
"allele_count_reference_population": 377,
"gnomad_exomes_af": 0.000247771,
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"gnomad_mito_homoplasmic": null,
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"computational_score_selected": 0.6842151880264282,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9959999918937683,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.744,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1942,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.686,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.79,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999995037813048,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 5,
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"pathogenic_score": 5,
"criteria": [
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"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000272321.12",
"gene_symbol": "WDPCP",
"hgnc_id": 28027,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.160G>A",
"hgvs_p": "p.Asp54Asn"
}
],
"clinvar_disease": "Bardet-Biedl syndrome,Bardet-Biedl syndrome 15,Heart defect - tongue hamartoma - polysyndactyly syndrome,Orofaciodigital syndrome,WDPCP-related disorder",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:2 US:4",
"phenotype_combined": "Heart defect - tongue hamartoma - polysyndactyly syndrome|Orofaciodigital syndrome|Bardet-Biedl syndrome|Bardet-Biedl syndrome 15;Heart defect - tongue hamartoma - polysyndactyly syndrome|WDPCP-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}