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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: 5-74721119-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=74721119&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 74721119,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000261416.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Cys",
"transcript": "NM_000521.4",
"protein_id": "NP_000512.2",
"transcript_support_level": null,
"aa_start": 539,
"aa_end": null,
"aa_length": 556,
"cds_start": 1615,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1643,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": "ENST00000261416.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Cys",
"transcript": "ENST00000261416.12",
"protein_id": "ENSP00000261416.7",
"transcript_support_level": 1,
"aa_start": 539,
"aa_end": null,
"aa_length": 556,
"cds_start": 1615,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1643,
"cdna_end": null,
"cdna_length": 1812,
"mane_select": "NM_000521.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.940C>T",
"hgvs_p": "p.Arg314Cys",
"transcript": "ENST00000511181.5",
"protein_id": "ENSP00000426285.1",
"transcript_support_level": 1,
"aa_start": 314,
"aa_end": null,
"aa_length": 331,
"cds_start": 940,
"cds_end": null,
"cds_length": 996,
"cdna_start": 1852,
"cdna_end": null,
"cdna_length": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.940C>T",
"hgvs_p": "p.Arg314Cys",
"transcript": "NM_001292004.2",
"protein_id": "NP_001278933.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 331,
"cds_start": 940,
"cds_end": null,
"cds_length": 996,
"cdna_start": 1852,
"cdna_end": null,
"cdna_length": 2021,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.550C>T",
"hgvs_p": "p.Arg184Cys",
"transcript": "ENST00000513336.5",
"protein_id": "ENSP00000423713.1",
"transcript_support_level": 3,
"aa_start": 184,
"aa_end": null,
"aa_length": 201,
"cds_start": 550,
"cds_end": null,
"cds_length": 606,
"cdna_start": 551,
"cdna_end": null,
"cdna_length": 720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "c.52C>T",
"hgvs_p": "p.Arg18Cys",
"transcript": "ENST00000509579.1",
"protein_id": "ENSP00000424939.1",
"transcript_support_level": 2,
"aa_start": 18,
"aa_end": null,
"aa_length": 35,
"cds_start": 52,
"cds_end": null,
"cds_length": 108,
"cdna_start": 637,
"cdna_end": null,
"cdna_length": 806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.334C>T",
"hgvs_p": null,
"transcript": "ENST00000513539.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 502,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.63C>T",
"hgvs_p": null,
"transcript": "ENST00000513867.1",
"protein_id": null,
"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": 711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.489-199C>T",
"hgvs_p": null,
"transcript": "ENST00000503312.5",
"protein_id": "ENSP00000426384.1",
"transcript_support_level": 5,
"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": 756,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"hgvs_c": "n.135-199C>T",
"hgvs_p": null,
"transcript": "ENST00000505859.1",
"protein_id": "ENSP00000424550.1",
"transcript_support_level": 3,
"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": 604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "NM_032380.5",
"protein_id": "NP_115756.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 779,
"cds_start": -4,
"cds_end": null,
"cds_length": 2340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": "ENST00000296805.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "ENST00000296805.8",
"protein_id": "ENSP00000296805.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 779,
"cds_start": -4,
"cds_end": null,
"cds_length": 2340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": "NM_032380.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "ENST00000509430.5",
"protein_id": "ENSP00000427004.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 779,
"cds_start": -4,
"cds_end": null,
"cds_length": 2340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "ENST00000345239.6",
"protein_id": "ENSP00000296804.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 732,
"cds_start": -4,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2856,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "NM_001281302.2",
"protein_id": "NP_001268231.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 811,
"cds_start": -4,
"cds_end": null,
"cds_length": 2436,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3111,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "NM_170691.3",
"protein_id": "NP_733792.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 732,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 2852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "n.*154G>A",
"hgvs_p": null,
"transcript": "ENST00000515125.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 1125,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "n.*87G>A",
"hgvs_p": null,
"transcript": "NR_104006.2",
"protein_id": null,
"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": 2854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "XM_017009986.2",
"protein_id": "XP_016865475.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 779,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 3319,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "XM_047417833.1",
"protein_id": "XP_047273789.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 779,
"cds_start": -4,
"cds_end": null,
"cds_length": 2340,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "XM_047417834.1",
"protein_id": "XP_047273790.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 732,
"cds_start": -4,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFM2",
"gene_hgnc_id": 29682,
"hgvs_c": "c.*536G>A",
"hgvs_p": null,
"transcript": "XM_047417835.1",
"protein_id": "XP_047273791.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 732,
"cds_start": -4,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HEXB",
"gene_hgnc_id": 4879,
"dbsnp": "rs749646826",
"frequency_reference_population": 0.000013680163,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000137352,
"gnomad_genomes_af": 0.0000131529,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8774305582046509,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.5799999833106995,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.874,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7885,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.55,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.803,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.598407014054932,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PM2",
"PP3_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000261416.12",
"gene_symbol": "HEXB",
"hgnc_id": 4879,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1615C>T",
"hgvs_p": "p.Arg539Cys"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000296805.8",
"gene_symbol": "GFM2",
"hgnc_id": 29682,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.*536G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Sandhoff disease",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Sandhoff disease",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}