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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: 12-57582631-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57582631&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2"
],
"effects": [
"splice_donor_variant",
"intron_variant"
],
"gene_symbol": "KIF5A",
"hgnc_id": 6323,
"hgvs_c": "c.3020+2T>A",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 10,
"score": 10,
"transcript": "NM_004984.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_score": 10,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.33,
"chr": "12",
"clinvar_classification": "risk factor",
"clinvar_disease": " 25, susceptibility to,Amyotrophic lateral sclerosis",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.33000001311302185,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1032,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5779,
"cdna_start": null,
"cds_end": null,
"cds_length": 3099,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_004984.4",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.3020+2T>A",
"hgvs_p": null,
"intron_rank": 27,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000455537.7",
"protein_coding": true,
"protein_id": "NP_004975.2",
"strand": true,
"transcript": "NM_004984.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1032,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5779,
"cdna_start": null,
"cds_end": null,
"cds_length": 3099,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000455537.7",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.3020+2T>A",
"hgvs_p": null,
"intron_rank": 27,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004984.4",
"protein_coding": true,
"protein_id": "ENSP00000408979.2",
"strand": true,
"transcript": "ENST00000455537.7",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 113,
"aa_ref": "Y",
"aa_start": 16,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3314,
"cdna_start": 47,
"cds_end": null,
"cds_length": 342,
"cds_start": 46,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000676437.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.46T>A",
"hgvs_p": "p.Tyr16Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502358.1",
"strand": true,
"transcript": "ENST00000676437.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1039,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5814,
"cdna_start": null,
"cds_end": null,
"cds_length": 3120,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 30,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000674619.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.3041+2T>A",
"hgvs_p": null,
"intron_rank": 28,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502270.1",
"strand": true,
"transcript": "ENST00000674619.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1032,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6790,
"cdna_start": null,
"cds_end": null,
"cds_length": 3099,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000938849.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.3020+2T>A",
"hgvs_p": null,
"intron_rank": 27,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000608908.1",
"strand": true,
"transcript": "ENST00000938849.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1031,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5795,
"cdna_start": null,
"cds_end": null,
"cds_length": 3096,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000910206.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.3017+2T>A",
"hgvs_p": null,
"intron_rank": 27,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580265.1",
"strand": true,
"transcript": "ENST00000910206.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1031,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5773,
"cdna_start": null,
"cds_end": null,
"cds_length": 3096,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000910207.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.3017+2T>A",
"hgvs_p": null,
"intron_rank": 27,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580266.1",
"strand": true,
"transcript": "ENST00000910207.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 997,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5572,
"cdna_start": null,
"cds_end": null,
"cds_length": 2994,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000676457.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.2915+2T>A",
"hgvs_p": null,
"intron_rank": 26,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501588.1",
"strand": true,
"transcript": "ENST00000676457.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 943,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5512,
"cdna_start": null,
"cds_end": null,
"cds_length": 2832,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001354705.2",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.2753+2T>A",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001341634.1",
"strand": true,
"transcript": "NM_001354705.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 943,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3527,
"cdna_start": null,
"cds_end": null,
"cds_length": 2832,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000286452.5",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.2753+2T>A",
"hgvs_p": null,
"intron_rank": 24,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000286452.5",
"strand": true,
"transcript": "ENST00000286452.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 67,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 629,
"cdna_start": null,
"cds_end": null,
"cds_length": 204,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000675697.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.83-470T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501809.1",
"strand": true,
"transcript": "ENST00000675697.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 10,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 459,
"cdna_start": null,
"cds_end": null,
"cds_length": 33,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000675866.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.26+2T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000502341.1",
"strand": true,
"transcript": "ENST00000675866.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 548,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000552227.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "n.305T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000552227.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3298,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000675737.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "n.1075T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000675737.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 5336,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000675882.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "n.2545T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000675882.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3286,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000675929.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "n.1580T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000675929.1",
"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": 150,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000675201.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "n.28+2T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000675201.1",
"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": 228,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000676265.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "n.28+2T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000676265.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 31,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 99,
"cdna_start": null,
"cds_end": null,
"cds_length": 98,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000676055.1",
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"hgvs_c": "c.*2T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000501739.1",
"strand": true,
"transcript": "ENST00000676055.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999988247793601,
"dbsnp": "rs1218712729",
"effect": "splice_donor_variant,intron_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 6323,
"gene_symbol": "KIF5A",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "risk factor",
"phenotype_combined": "Amyotrophic lateral sclerosis, susceptibility to, 25",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.618,
"pos": 57582631,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.949999988079071,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.69,
"transcript": "NM_004984.4"
}
]
}