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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: 10-32015558-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=32015558&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 8,
"criteria": [
"BP4_Strong",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "KIF5B",
"hgnc_id": 6324,
"hgvs_c": "c.2863G>A",
"hgvs_p": "p.Val955Met",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -8,
"transcript": "NM_004521.3",
"verdict": "Benign"
},
{
"benign_score": 4,
"criteria": [
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC107984219",
"hgnc_id": null,
"hgvs_c": "n.5354-2468C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -4,
"transcript": "XR_001747415.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_score": -8,
"allele_count_reference_population": 16,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1315,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.4,
"chr": "10",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.04404407739639282,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 963,
"aa_ref": "V",
"aa_start": 955,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5866,
"cdna_start": 3315,
"cds_end": null,
"cds_length": 2892,
"cds_start": 2863,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "NM_004521.3",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.2863G>A",
"hgvs_p": "p.Val955Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000302418.5",
"protein_coding": true,
"protein_id": "NP_004512.1",
"strand": false,
"transcript": "NM_004521.3",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 963,
"aa_ref": "V",
"aa_start": 955,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5866,
"cdna_start": 3315,
"cds_end": null,
"cds_length": 2892,
"cds_start": 2863,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000302418.5",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.2863G>A",
"hgvs_p": "p.Val955Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004521.3",
"protein_coding": true,
"protein_id": "ENSP00000307078.4",
"strand": false,
"transcript": "ENST00000302418.5",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 1058,
"aa_ref": "V",
"aa_start": 1050,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4017,
"cdna_start": 3590,
"cds_end": null,
"cds_length": 3177,
"cds_start": 3148,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861449.1",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.3148G>A",
"hgvs_p": "p.Val1050Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531508.1",
"strand": false,
"transcript": "ENST00000861449.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 962,
"aa_ref": "V",
"aa_start": 954,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5027,
"cdna_start": 3312,
"cds_end": null,
"cds_length": 2889,
"cds_start": 2860,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "ENST00000861448.1",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.2860G>A",
"hgvs_p": "p.Val954Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000531507.1",
"strand": false,
"transcript": "ENST00000861448.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 928,
"aa_ref": "V",
"aa_start": 920,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5785,
"cdna_start": 3239,
"cds_end": null,
"cds_length": 2787,
"cds_start": 2758,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000948543.1",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.2758G>A",
"hgvs_p": "p.Val920Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618602.1",
"strand": false,
"transcript": "ENST00000948543.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 915,
"aa_ref": "V",
"aa_start": 907,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5722,
"cdna_start": 3170,
"cds_end": null,
"cds_length": 2748,
"cds_start": 2719,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000948544.1",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.2719G>A",
"hgvs_p": "p.Val907Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000618603.1",
"strand": false,
"transcript": "ENST00000948544.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 963,
"aa_ref": "V",
"aa_start": 955,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3366,
"cdna_start": 3315,
"cds_end": null,
"cds_length": 2892,
"cds_start": 2863,
"consequences": [
"missense_variant"
],
"exon_count": 25,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "XM_047425202.1",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.2863G>A",
"hgvs_p": "p.Val955Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047281158.1",
"strand": false,
"transcript": "XM_047425202.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 869,
"aa_ref": "V",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6080,
"cdna_start": 3529,
"cds_end": null,
"cds_length": 2610,
"cds_start": 2581,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 26,
"exon_rank_end": null,
"feature": "XM_047425203.1",
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"hgvs_c": "c.2581G>A",
"hgvs_p": "p.Val861Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047281159.1",
"strand": false,
"transcript": "XM_047425203.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 7727,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001747415.2",
"gene_hgnc_id": null,
"gene_symbol": "LOC107984219",
"hgvs_c": "n.5354-2468C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_001747415.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs772124743",
"effect": "missense_variant",
"frequency_reference_population": 0.000009918926,
"gene_hgnc_id": 6324,
"gene_symbol": "KIF5B",
"gnomad_exomes_ac": 13,
"gnomad_exomes_af": 0.00000889905,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197047,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.467,
"pos": 32015558,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.098,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_004521.3"
}
]
}