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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: 11-64854734-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=64854734&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "EHD1",
"hgnc_id": 3242,
"hgvs_c": "c.1246T>A",
"hgvs_p": "p.Ser416Thr",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_001282445.2",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "ENSG00000293953",
"hgnc_id": null,
"hgvs_c": "n.-173A>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000720083.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.0617,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.6,
"chr": "11",
"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": 0.06359609961509705,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 534,
"aa_ref": "S",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4453,
"cdna_start": 1361,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1204,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_006795.4",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.1204T>A",
"hgvs_p": "p.Ser402Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000320631.8",
"protein_coding": true,
"protein_id": "NP_006786.2",
"strand": false,
"transcript": "NM_006795.4",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 534,
"aa_ref": "S",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4453,
"cdna_start": 1361,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1204,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000320631.8",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.1204T>A",
"hgvs_p": "p.Ser402Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006795.4",
"protein_coding": true,
"protein_id": "ENSP00000320516.3",
"strand": false,
"transcript": "ENST00000320631.8",
"transcript_support_level": 1
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 548,
"aa_ref": "S",
"aa_start": 416,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4401,
"cdna_start": 1309,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1246,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001282445.2",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.1246T>A",
"hgvs_p": "p.Ser416Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001269374.1",
"strand": false,
"transcript": "NM_001282445.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 548,
"aa_ref": "S",
"aa_start": 416,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3336,
"cdna_start": 1329,
"cds_end": null,
"cds_length": 1647,
"cds_start": 1246,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000621096.4",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.1246T>A",
"hgvs_p": "p.Ser416Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479153.1",
"strand": false,
"transcript": "ENST00000621096.4",
"transcript_support_level": 5
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 534,
"aa_ref": "S",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4723,
"cdna_start": 1631,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1204,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001282444.2",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.1204T>A",
"hgvs_p": "p.Ser402Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001269373.1",
"strand": false,
"transcript": "NM_001282444.2",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 534,
"aa_ref": "S",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3618,
"cdna_start": 1615,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1204,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000359393.6",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.1204T>A",
"hgvs_p": "p.Ser402Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000352354.2",
"strand": false,
"transcript": "ENST00000359393.6",
"transcript_support_level": 2
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 534,
"aa_ref": "S",
"aa_start": 402,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3375,
"cdna_start": 1372,
"cds_end": null,
"cds_length": 1605,
"cds_start": 1204,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000909783.1",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.1204T>A",
"hgvs_p": "p.Ser402Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579842.1",
"strand": false,
"transcript": "ENST00000909783.1",
"transcript_support_level": null
},
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 305,
"aa_ref": "S",
"aa_start": 266,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1015,
"cdna_start": 893,
"cds_end": null,
"cds_length": 918,
"cds_start": 796,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000421510.5",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "c.796T>A",
"hgvs_p": "p.Ser266Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000391429.1",
"strand": false,
"transcript": "ENST00000421510.5",
"transcript_support_level": 3
},
{
"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": 3469,
"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": "ENST00000484846.1",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "n.1466T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000484846.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 648,
"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": "ENST00000488711.1",
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"hgvs_c": "n.206T>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000488711.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 594,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000720083.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000293953",
"hgvs_c": "n.-173A>T",
"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": "ENST00000720083.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": 6.849897e-7,
"gene_hgnc_id": 3242,
"gene_symbol": "EHD1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.8499e-7,
"gnomad_exomes_homalt": 0,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.185,
"pos": 64854734,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.017,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001282445.2"
}
]
}