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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: 5-160565579-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=160565579&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 160565579,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000327245.10",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His",
"transcript": "NM_025153.3",
"protein_id": "NP_079429.2",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4260,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 5106,
"cdna_end": null,
"cdna_length": 7565,
"mane_select": "ENST00000327245.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His",
"transcript": "ENST00000327245.10",
"protein_id": "ENSP00000313600.5",
"transcript_support_level": 1,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4260,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 5106,
"cdna_end": null,
"cdna_length": 7565,
"mane_select": "NM_025153.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His",
"transcript": "NM_001366652.1",
"protein_id": "NP_001353581.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4260,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4745,
"cdna_end": null,
"cdna_length": 7204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His",
"transcript": "NM_001366655.1",
"protein_id": "NP_001353584.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4260,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4922,
"cdna_end": null,
"cdna_length": 7381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4224A>T",
"hgvs_p": "p.Gln1408His",
"transcript": "NM_001366657.1",
"protein_id": "NP_001353586.1",
"transcript_support_level": null,
"aa_start": 1408,
"aa_end": null,
"aa_length": 1449,
"cds_start": 4224,
"cds_end": null,
"cds_length": 4350,
"cdna_start": 4886,
"cdna_end": null,
"cdna_length": 7345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4176A>T",
"hgvs_p": "p.Gln1392His",
"transcript": "NM_001410822.1",
"protein_id": "NP_001397751.1",
"transcript_support_level": null,
"aa_start": 1392,
"aa_end": null,
"aa_length": 1433,
"cds_start": 4176,
"cds_end": null,
"cds_length": 4302,
"cdna_start": 4347,
"cdna_end": null,
"cdna_length": 6806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4176A>T",
"hgvs_p": "p.Gln1392His",
"transcript": "ENST00000642502.1",
"protein_id": "ENSP00000493802.1",
"transcript_support_level": null,
"aa_start": 1392,
"aa_end": null,
"aa_length": 1433,
"cds_start": 4176,
"cds_end": null,
"cds_length": 4302,
"cdna_start": 4341,
"cdna_end": null,
"cdna_length": 6800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His",
"transcript": "XM_011534468.3",
"protein_id": "XP_011532770.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4260,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4613,
"cdna_end": null,
"cdna_length": 7072,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His",
"transcript": "XM_011534469.2",
"protein_id": "XP_011532771.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4260,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4929,
"cdna_end": null,
"cdna_length": 7388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His",
"transcript": "XM_047416994.1",
"protein_id": "XP_047272950.1",
"transcript_support_level": null,
"aa_start": 1420,
"aa_end": null,
"aa_length": 1461,
"cds_start": 4260,
"cds_end": null,
"cds_length": 4386,
"cdna_start": 4739,
"cdna_end": null,
"cdna_length": 7198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4224A>T",
"hgvs_p": "p.Gln1408His",
"transcript": "XM_017009252.2",
"protein_id": "XP_016864741.1",
"transcript_support_level": null,
"aa_start": 1408,
"aa_end": null,
"aa_length": 1449,
"cds_start": 4224,
"cds_end": null,
"cds_length": 4350,
"cdna_start": 4577,
"cdna_end": null,
"cdna_length": 7036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.4059A>T",
"hgvs_p": "p.Gln1353His",
"transcript": "XM_047416995.1",
"protein_id": "XP_047272951.1",
"transcript_support_level": null,
"aa_start": 1353,
"aa_end": null,
"aa_length": 1394,
"cds_start": 4059,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 4412,
"cdna_end": null,
"cdna_length": 6871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"hgvs_c": "c.3975A>T",
"hgvs_p": "p.Gln1325His",
"transcript": "XM_047416996.1",
"protein_id": "XP_047272952.1",
"transcript_support_level": null,
"aa_start": 1325,
"aa_end": null,
"aa_length": 1366,
"cds_start": 3975,
"cds_end": null,
"cds_length": 4101,
"cdna_start": 4146,
"cdna_end": null,
"cdna_length": 6605,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.658-35130T>A",
"hgvs_p": null,
"transcript": "ENST00000770454.1",
"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": 914,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.563-35130T>A",
"hgvs_p": null,
"transcript": "ENST00000770455.1",
"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": 818,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.340+12986T>A",
"hgvs_p": null,
"transcript": "ENST00000770456.1",
"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": 594,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MIR3142HG",
"gene_hgnc_id": 51944,
"hgvs_c": "n.317+12986T>A",
"hgvs_p": null,
"transcript": "ENST00000770457.1",
"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": 574,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP10B",
"gene_hgnc_id": 13543,
"dbsnp": "rs768749730",
"frequency_reference_population": 0.000032840195,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000123133,
"gnomad_genomes_af": 0.000230193,
"gnomad_exomes_ac": 18,
"gnomad_genomes_ac": 35,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.030699491500854492,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0932,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.428,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000327245.10",
"gene_symbol": "ATP10B",
"hgnc_id": 13543,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4260A>T",
"hgvs_p": "p.Gln1420His"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000770454.1",
"gene_symbol": "MIR3142HG",
"hgnc_id": 51944,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.658-35130T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}