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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: 8-38176942-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=38176942&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "BAG4",
"hgnc_id": 940,
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -10,
"transcript": "NM_004874.4",
"verdict": "Benign"
},
{
"benign_score": 10,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"effects": [
"upstream_gene_variant"
],
"gene_symbol": "LSM1",
"hgnc_id": 20472,
"hgvs_c": "n.-212C>T",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -10,
"transcript": "ENST00000520286.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_score": -10,
"allele_count_reference_population": 5652,
"alphamissense_prediction": null,
"alphamissense_score": 0.0899,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.13,
"chr": "8",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.00678446888923645,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 457,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4197,
"cdna_start": 88,
"cds_end": null,
"cds_length": 1374,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_004874.4",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000287322.5",
"protein_coding": true,
"protein_id": "NP_004865.1",
"strand": true,
"transcript": "NM_004874.4",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 457,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4197,
"cdna_start": 88,
"cds_end": null,
"cds_length": 1374,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000287322.5",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004874.4",
"protein_coding": true,
"protein_id": "ENSP00000287322.4",
"strand": true,
"transcript": "ENST00000287322.5",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 421,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1943,
"cdna_start": 355,
"cds_end": null,
"cds_length": 1266,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000432471.6",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000393298.2",
"strand": true,
"transcript": "ENST00000432471.6",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 421,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4089,
"cdna_start": 88,
"cds_end": null,
"cds_length": 1266,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_001204878.2",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001191807.1",
"strand": true,
"transcript": "NM_001204878.2",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 393,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4003,
"cdna_start": 86,
"cds_end": null,
"cds_length": 1182,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000931320.1",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601379.1",
"strand": true,
"transcript": "ENST00000931320.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 392,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3996,
"cdna_start": 92,
"cds_end": null,
"cds_length": 1179,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000931321.1",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601380.1",
"strand": true,
"transcript": "ENST00000931321.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 372,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2029,
"cdna_start": 80,
"cds_end": null,
"cds_length": 1119,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000931322.1",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601381.1",
"strand": true,
"transcript": "ENST00000931322.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 336,
"aa_ref": "G",
"aa_start": 25,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3837,
"cdna_start": 96,
"cds_end": null,
"cds_length": 1011,
"cds_start": 73,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000931319.1",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "c.73G>A",
"hgvs_p": "p.Gly25Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601378.1",
"strand": true,
"transcript": "ENST00000931319.1",
"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": 530,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000521282.1",
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"hgvs_c": "n.58-63G>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": "ENST00000521282.1",
"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": 776,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000520286.5",
"gene_hgnc_id": 20472,
"gene_symbol": "LSM1",
"hgvs_c": "n.-212C>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": "ENST00000520286.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1568,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000522515.5",
"gene_hgnc_id": 20472,
"gene_symbol": "LSM1",
"hgvs_c": "n.-226C>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": "ENST00000522515.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 883,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_045493.1",
"gene_hgnc_id": 20472,
"gene_symbol": "LSM1",
"hgvs_c": "n.-212C>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": "NR_045493.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs61731142",
"effect": "missense_variant",
"frequency_reference_population": 0.0036333574,
"gene_hgnc_id": 940,
"gene_symbol": "BAG4",
"gnomad_exomes_ac": 5203,
"gnomad_exomes_af": 0.00370793,
"gnomad_exomes_homalt": 16,
"gnomad_genomes_ac": 449,
"gnomad_genomes_af": 0.00294666,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 17,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.155,
"pos": 38176942,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.276,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004874.4"
}
]
}