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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: 15-41900941-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=41900941&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "EHD4",
"hgnc_id": 3245,
"hgvs_c": "c.1330G>A",
"hgvs_p": "p.Val444Met",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_139265.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 118,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.8881,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.2,
"chr": "15",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5569477081298828,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 541,
"aa_ref": "V",
"aa_start": 444,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6401,
"cdna_start": 1393,
"cds_end": null,
"cds_length": 1626,
"cds_start": 1330,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_139265.4",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1330G>A",
"hgvs_p": "p.Val444Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000220325.9",
"protein_coding": true,
"protein_id": "NP_644670.1",
"strand": false,
"transcript": "NM_139265.4",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 541,
"aa_ref": "V",
"aa_start": 444,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6401,
"cdna_start": 1393,
"cds_end": null,
"cds_length": 1626,
"cds_start": 1330,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000220325.9",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1330G>A",
"hgvs_p": "p.Val444Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_139265.4",
"protein_coding": true,
"protein_id": "ENSP00000220325.4",
"strand": false,
"transcript": "ENST00000220325.9",
"transcript_support_level": 1
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 579,
"aa_ref": "V",
"aa_start": 482,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2990,
"cdna_start": 1490,
"cds_end": null,
"cds_length": 1740,
"cds_start": 1444,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000857506.1",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1444G>A",
"hgvs_p": "p.Val482Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527565.1",
"strand": false,
"transcript": "ENST00000857506.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 539,
"aa_ref": "V",
"aa_start": 442,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2928,
"cdna_start": 1423,
"cds_end": null,
"cds_length": 1620,
"cds_start": 1324,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000926747.1",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1324G>A",
"hgvs_p": "p.Val442Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596806.1",
"strand": false,
"transcript": "ENST00000926747.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 536,
"aa_ref": "V",
"aa_start": 439,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2874,
"cdna_start": 1376,
"cds_end": null,
"cds_length": 1611,
"cds_start": 1315,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000952467.1",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1315G>A",
"hgvs_p": "p.Val439Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622526.1",
"strand": false,
"transcript": "ENST00000952467.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 486,
"aa_ref": "V",
"aa_start": 389,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2415,
"cdna_start": 1225,
"cds_end": null,
"cds_length": 1461,
"cds_start": 1165,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000857507.1",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1165G>A",
"hgvs_p": "p.Val389Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000527566.1",
"strand": false,
"transcript": "ENST00000857507.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 482,
"aa_ref": "V",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3783,
"cdna_start": 1226,
"cds_end": null,
"cds_length": 1449,
"cds_start": 1153,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000952466.1",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1153G>A",
"hgvs_p": "p.Val385Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000622525.1",
"strand": false,
"transcript": "ENST00000952466.1",
"transcript_support_level": null
},
{
"aa_alt": "M",
"aa_end": null,
"aa_length": 453,
"aa_ref": "V",
"aa_start": 356,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6230,
"cdna_start": 1222,
"cds_end": null,
"cds_length": 1362,
"cds_start": 1066,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047432408.1",
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"hgvs_c": "c.1066G>A",
"hgvs_p": "p.Val356Met",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288364.1",
"strand": false,
"transcript": "XM_047432408.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199610689",
"effect": "missense_variant",
"frequency_reference_population": 0.00007312161,
"gene_hgnc_id": 3245,
"gene_symbol": "EHD4",
"gnomad_exomes_ac": 105,
"gnomad_exomes_af": 0.0000718394,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 13,
"gnomad_genomes_af": 0.0000854386,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.108,
"pos": 41900941,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.325,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_139265.4"
}
]
}