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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: 1-11790699-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11790699&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 11790699,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001330358.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1952G>A",
"hgvs_p": "p.Arg651Lys",
"transcript": "NM_005957.5",
"protein_id": "NP_005948.3",
"transcript_support_level": null,
"aa_start": 651,
"aa_end": null,
"aa_length": 656,
"cds_start": 1952,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000376590.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005957.5"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1952G>A",
"hgvs_p": "p.Arg651Lys",
"transcript": "ENST00000376590.9",
"protein_id": "ENSP00000365775.3",
"transcript_support_level": 1,
"aa_start": 651,
"aa_end": null,
"aa_length": 656,
"cds_start": 1952,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005957.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376590.9"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.2072G>A",
"hgvs_p": "p.Arg691Lys",
"transcript": "ENST00000423400.7",
"protein_id": "ENSP00000398908.3",
"transcript_support_level": 1,
"aa_start": 691,
"aa_end": null,
"aa_length": 696,
"cds_start": 2072,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000423400.7"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1952G>A",
"hgvs_p": "p.Arg651Lys",
"transcript": "ENST00000376592.6",
"protein_id": "ENSP00000365777.1",
"transcript_support_level": 1,
"aa_start": 651,
"aa_end": null,
"aa_length": 656,
"cds_start": 1952,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376592.6"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.2075G>A",
"hgvs_p": "p.Arg692Lys",
"transcript": "NM_001330358.2",
"protein_id": "NP_001317287.1",
"transcript_support_level": null,
"aa_start": 692,
"aa_end": null,
"aa_length": 697,
"cds_start": 2075,
"cds_end": null,
"cds_length": 2094,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330358.2"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.2075G>A",
"hgvs_p": "p.Arg692Lys",
"transcript": "ENST00000376583.7",
"protein_id": "ENSP00000365767.3",
"transcript_support_level": 5,
"aa_start": 692,
"aa_end": null,
"aa_length": 697,
"cds_start": 2075,
"cds_end": null,
"cds_length": 2094,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376583.7"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.2075G>A",
"hgvs_p": "p.Arg692Lys",
"transcript": "ENST00000376585.6",
"protein_id": "ENSP00000365770.1",
"transcript_support_level": 5,
"aa_start": 692,
"aa_end": null,
"aa_length": 697,
"cds_start": 2075,
"cds_end": null,
"cds_length": 2094,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376585.6"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.2072G>A",
"hgvs_p": "p.Arg691Lys",
"transcript": "NM_001410750.1",
"protein_id": "NP_001397679.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 696,
"cds_start": 2072,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410750.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1973G>A",
"hgvs_p": "p.Arg658Lys",
"transcript": "ENST00000970342.1",
"protein_id": "ENSP00000640401.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 663,
"cds_start": 1973,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970342.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1952G>A",
"hgvs_p": "p.Arg651Lys",
"transcript": "ENST00000911085.1",
"protein_id": "ENSP00000581144.1",
"transcript_support_level": null,
"aa_start": 651,
"aa_end": null,
"aa_length": 656,
"cds_start": 1952,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911085.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1802G>A",
"hgvs_p": "p.Arg601Lys",
"transcript": "ENST00000911084.1",
"protein_id": "ENSP00000581143.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 606,
"cds_start": 1802,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911084.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1802G>A",
"hgvs_p": "p.Arg601Lys",
"transcript": "ENST00000911086.1",
"protein_id": "ENSP00000581145.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 606,
"cds_start": 1802,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911086.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1802G>A",
"hgvs_p": "p.Arg601Lys",
"transcript": "ENST00000911087.1",
"protein_id": "ENSP00000581146.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 606,
"cds_start": 1802,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911087.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1802G>A",
"hgvs_p": "p.Arg601Lys",
"transcript": "ENST00000970341.1",
"protein_id": "ENSP00000640400.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 606,
"cds_start": 1802,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970341.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1769G>A",
"hgvs_p": "p.Arg590Lys",
"transcript": "ENST00000970343.1",
"protein_id": "ENSP00000640402.1",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 595,
"cds_start": 1769,
"cds_end": null,
"cds_length": 1788,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970343.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1217G>A",
"hgvs_p": "p.Arg406Lys",
"transcript": "ENST00000641820.1",
"protein_id": "ENSP00000492937.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 411,
"cds_start": 1217,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641820.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1952G>A",
"hgvs_p": "p.Arg651Lys",
"transcript": "XM_005263462.5",
"protein_id": "XP_005263519.1",
"transcript_support_level": null,
"aa_start": 651,
"aa_end": null,
"aa_length": 656,
"cds_start": 1952,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005263462.5"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1952G>A",
"hgvs_p": "p.Arg651Lys",
"transcript": "XM_047421178.1",
"protein_id": "XP_047277134.1",
"transcript_support_level": null,
"aa_start": 651,
"aa_end": null,
"aa_length": 656,
"cds_start": 1952,
"cds_end": null,
"cds_length": 1971,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421178.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1925G>A",
"hgvs_p": "p.Arg642Lys",
"transcript": "XM_017001328.3",
"protein_id": "XP_016856817.1",
"transcript_support_level": null,
"aa_start": 642,
"aa_end": null,
"aa_length": 647,
"cds_start": 1925,
"cds_end": null,
"cds_length": 1944,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017001328.3"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1802G>A",
"hgvs_p": "p.Arg601Lys",
"transcript": "XM_047421180.1",
"protein_id": "XP_047277136.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 606,
"cds_start": 1802,
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"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421180.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1802G>A",
"hgvs_p": "p.Arg601Lys",
"transcript": "XM_047421181.1",
"protein_id": "XP_047277137.1",
"transcript_support_level": null,
"aa_start": 601,
"aa_end": null,
"aa_length": 606,
"cds_start": 1802,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421181.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.1706G>A",
"hgvs_p": "p.Arg569Lys",
"transcript": "XM_005263463.5",
"protein_id": "XP_005263520.1",
"transcript_support_level": null,
"aa_start": 569,
"aa_end": null,
"aa_length": 574,
"cds_start": 1706,
"cds_end": null,
"cds_length": 1725,
"cdna_start": null,
"cdna_end": null,
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"mane_select": null,
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],
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"computational_score_selected": 0.0745019018650055,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.159,
"revel_prediction": "Benign",
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"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.207,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"spliceai_max_prediction": "Benign",
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"apogee2_score": null,
"apogee2_prediction": null,
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"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
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"pathogenic_score": 2,
"criteria": [
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"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001330358.2",
"gene_symbol": "MTHFR",
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"effects": [
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],
"inheritance_mode": "AR",
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}
],
"clinvar_disease": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Homocystinuria due to methylene tetrahydrofolate reductase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}