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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: 1-11796321-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=11796321&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 11796321,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001330358.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "NM_005957.5",
"protein_id": "NP_005948.3",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 656,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000376590.9",
"protein_id": "ENSP00000365775.3",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 656,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Ala262Val",
"transcript": "ENST00000423400.7",
"protein_id": "ENSP00000398908.3",
"transcript_support_level": 1,
"aa_start": 262,
"aa_end": null,
"aa_length": 696,
"cds_start": 785,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000376592.6",
"protein_id": "ENSP00000365777.1",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 656,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000376486.3",
"protein_id": "ENSP00000365669.3",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 228,
"cds_start": 665,
"cds_end": null,
"cds_length": 689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376486.3"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Ala263Val",
"transcript": "NM_001330358.2",
"protein_id": "NP_001317287.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 697,
"cds_start": 788,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Ala263Val",
"transcript": "ENST00000376583.7",
"protein_id": "ENSP00000365767.3",
"transcript_support_level": 5,
"aa_start": 263,
"aa_end": null,
"aa_length": 697,
"cds_start": 788,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Ala263Val",
"transcript": "ENST00000376585.6",
"protein_id": "ENSP00000365770.1",
"transcript_support_level": 5,
"aa_start": 263,
"aa_end": null,
"aa_length": 697,
"cds_start": 788,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Ala262Val",
"transcript": "NM_001410750.1",
"protein_id": "NP_001397679.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 696,
"cds_start": 785,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000970342.1",
"protein_id": "ENSP00000640401.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 663,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000911085.1",
"protein_id": "ENSP00000581144.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 656,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000641407.1",
"protein_id": "ENSP00000493098.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 642,
"cds_start": 665,
"cds_end": null,
"cds_length": 1929,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000641407.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000911084.1",
"protein_id": "ENSP00000581143.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 606,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000911086.1",
"protein_id": "ENSP00000581145.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 606,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000911087.1",
"protein_id": "ENSP00000581146.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 606,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000970341.1",
"protein_id": "ENSP00000640400.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 606,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "ENST00000970343.1",
"protein_id": "ENSP00000640402.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 595,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Ala263Val",
"transcript": "XM_011541496.4",
"protein_id": "XP_011539798.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 683,
"cds_start": 788,
"cds_end": null,
"cds_length": 2052,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541496.4"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.785C>T",
"hgvs_p": "p.Ala262Val",
"transcript": "XM_047421174.1",
"protein_id": "XP_047277130.1",
"transcript_support_level": null,
"aa_start": 262,
"aa_end": null,
"aa_length": 682,
"cds_start": 785,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047421174.1"
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "XM_005263462.5",
"protein_id": "XP_005263519.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 656,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ala222Val",
"transcript": "XM_047421178.1",
"protein_id": "XP_047277134.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 656,
"cds_start": 665,
"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": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFR",
"gene_hgnc_id": 7436,
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Ala263Val",
"transcript": "XM_017001328.3",
"protein_id": "XP_016856817.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 647,
"cds_start": 788,
"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"
},
{
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],
"gene_symbol": "MTHFR",
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"dbsnp": "rs1801133",
"frequency_reference_population": 0.31821376,
"hom_count_reference_population": 87723,
"allele_count_reference_population": 513548,
"gnomad_exomes_af": 0.322692,
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"gnomad_exomes_ac": 471698,
"gnomad_genomes_ac": 41850,
"gnomad_exomes_homalt": 80805,
"gnomad_genomes_homalt": 6918,
"gnomad_mito_homoplasmic": null,
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"computational_score_selected": 0.001652747392654419,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.842,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6324,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.137,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,PP3,BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 12,
"pathogenic_score": 3,
"criteria": [
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"PP3",
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001330358.2",
"gene_symbol": "MTHFR",
"hgnc_id": 7436,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.788C>T",
"hgvs_p": "p.Ala263Val"
}
],
"clinvar_disease": " folate-sensitive,Gastrointestinal stromal tumor,Homocystinuria due to methylene tetrahydrofolate reductase deficiency,MTHFR THERMOLABILE POLYMORPHISM,Neural tube defects,See cases,Thrombophilia due to thrombin defect,methotrexate response - Toxicity,not provided,not specified",
"clinvar_classification": "drug response",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:2 US:3 LB:1 B:2 O:3",
"phenotype_combined": "MTHFR THERMOLABILE POLYMORPHISM|Gastrointestinal stromal tumor|Neural tube defects, folate-sensitive|not specified|not provided|Homocystinuria due to methylene tetrahydrofolate reductase deficiency|Thrombophilia due to thrombin defect|methotrexate response - Toxicity|See cases",
"pathogenicity_classification_combined": "drug response",
"custom_annotations": null
}
],
"message": null
}