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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: 3-170998299-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=170998299&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 170998299,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000340.2",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1268T>A",
"hgvs_p": "p.Val423Glu",
"transcript": "NM_000340.2",
"protein_id": "NP_000331.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 524,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000314251.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000340.2"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1268T>A",
"hgvs_p": "p.Val423Glu",
"transcript": "ENST00000314251.8",
"protein_id": "ENSP00000323568.3",
"transcript_support_level": 1,
"aa_start": 423,
"aa_end": null,
"aa_length": 524,
"cds_start": 1268,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000340.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000314251.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*735T>A",
"hgvs_p": null,
"transcript": "ENST00000497642.5",
"protein_id": "ENSP00000418456.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000497642.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*735T>A",
"hgvs_p": null,
"transcript": "ENST00000497642.5",
"protein_id": "ENSP00000418456.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000497642.5"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1265T>A",
"hgvs_p": "p.Val422Glu",
"transcript": "ENST00000878399.1",
"protein_id": "ENSP00000548458.1",
"transcript_support_level": null,
"aa_start": 422,
"aa_end": null,
"aa_length": 523,
"cds_start": 1265,
"cds_end": null,
"cds_length": 1572,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878399.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1175T>A",
"hgvs_p": "p.Val392Glu",
"transcript": "ENST00000878398.1",
"protein_id": "ENSP00000548457.1",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 493,
"cds_start": 1175,
"cds_end": null,
"cds_length": 1482,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878398.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1115T>A",
"hgvs_p": "p.Val372Glu",
"transcript": "ENST00000878397.1",
"protein_id": "ENSP00000548456.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 473,
"cds_start": 1115,
"cds_end": null,
"cds_length": 1422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878397.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1100T>A",
"hgvs_p": "p.Val367Glu",
"transcript": "ENST00000878402.1",
"protein_id": "ENSP00000548461.1",
"transcript_support_level": null,
"aa_start": 367,
"aa_end": null,
"aa_length": 468,
"cds_start": 1100,
"cds_end": null,
"cds_length": 1407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878402.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1043T>A",
"hgvs_p": "p.Val348Glu",
"transcript": "ENST00000878401.1",
"protein_id": "ENSP00000548460.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 449,
"cds_start": 1043,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878401.1"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.911T>A",
"hgvs_p": "p.Val304Glu",
"transcript": "NM_001278658.2",
"protein_id": "NP_001265587.1",
"transcript_support_level": null,
"aa_start": 304,
"aa_end": null,
"aa_length": 405,
"cds_start": 911,
"cds_end": null,
"cds_length": 1218,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278658.2"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.749T>A",
"hgvs_p": "p.Val250Glu",
"transcript": "NM_001278659.2",
"protein_id": "NP_001265588.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 351,
"cds_start": 749,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001278659.2"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1223T>A",
"hgvs_p": "p.Val408Glu",
"transcript": "XM_011513087.3",
"protein_id": "XP_011511389.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 509,
"cds_start": 1223,
"cds_end": null,
"cds_length": 1530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513087.3"
},
{
"aa_ref": "V",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.749T>A",
"hgvs_p": "p.Val250Glu",
"transcript": "XM_047448761.1",
"protein_id": "XP_047304717.1",
"transcript_support_level": null,
"aa_start": 250,
"aa_end": null,
"aa_length": 351,
"cds_start": 749,
"cds_end": null,
"cds_length": 1056,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047448761.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1171-196T>A",
"hgvs_p": null,
"transcript": "ENST00000878396.1",
"protein_id": "ENSP00000548455.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 456,
"cds_start": null,
"cds_end": null,
"cds_length": 1371,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878396.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "c.1069-196T>A",
"hgvs_p": null,
"transcript": "ENST00000878400.1",
"protein_id": "ENSP00000548459.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 422,
"cds_start": null,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878400.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*735T>A",
"hgvs_p": null,
"transcript": "ENST00000469787.1",
"protein_id": "ENSP00000417918.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000469787.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"hgvs_c": "n.*735T>A",
"hgvs_p": null,
"transcript": "ENST00000469787.1",
"protein_id": "ENSP00000417918.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000469787.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.291+3274A>T",
"hgvs_p": null,
"transcript": "ENST00000655926.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000655926.1"
},
{
"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": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.309+3274A>T",
"hgvs_p": null,
"transcript": "ENST00000834079.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000834079.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.476+3274A>T",
"hgvs_p": null,
"transcript": "ENST00000834080.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000834080.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.486+3274A>T",
"hgvs_p": null,
"transcript": "ENST00000834081.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000834081.1"
},
{
"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": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.484+3274A>T",
"hgvs_p": null,
"transcript": "ENST00000834082.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000834082.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286856",
"gene_hgnc_id": null,
"hgvs_c": "n.448+3274A>T",
"hgvs_p": null,
"transcript": "ENST00000834083.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000834083.1"
}
],
"gene_symbol": "SLC2A2",
"gene_hgnc_id": 11006,
"dbsnp": "rs28928874",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9597141742706299,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.907,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8156,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.103,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.03,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_000340.2",
"gene_symbol": "SLC2A2",
"hgnc_id": 11006,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1268T>A",
"hgvs_p": "p.Val423Glu"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000655926.1",
"gene_symbol": "ENSG00000286856",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.291+3274A>T",
"hgvs_p": null
}
],
"clinvar_disease": "Fanconi-Bickel syndrome",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Fanconi-Bickel syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}