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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: 3-52362504-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=52362504&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"PP3",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "DNAH1",
"hgnc_id": 2940,
"hgvs_c": "c.5094+3A>T",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 1,
"score": -15,
"transcript": "NM_015512.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP6_Very_Strong,BS1,BS2",
"acmg_score": -15,
"allele_count_reference_population": 1045,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"chr": "3",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " 37, primary,Ciliary dyskinesia,DNAH1-related disorder,Spermatogenic failure 18,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7300000190734863,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 4265,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 13105,
"cdna_start": null,
"cds_end": null,
"cds_length": 12798,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 78,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_015512.5",
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"hgvs_c": "c.5094+3A>T",
"hgvs_p": null,
"intron_rank": 31,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000420323.7",
"protein_coding": true,
"protein_id": "NP_056327.4",
"strand": true,
"transcript": "NM_015512.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 4265,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 13105,
"cdna_start": null,
"cds_end": null,
"cds_length": 12798,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 78,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000420323.7",
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"hgvs_c": "c.5094+3A>T",
"hgvs_p": null,
"intron_rank": 31,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015512.5",
"protein_coding": true,
"protein_id": "ENSP00000401514.2",
"strand": true,
"transcript": "ENST00000420323.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 4288,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 18153,
"cdna_start": null,
"cds_end": null,
"cds_length": 12867,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 80,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017006129.2",
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"hgvs_c": "c.5094+3A>T",
"hgvs_p": null,
"intron_rank": 32,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861618.1",
"strand": true,
"transcript": "XM_017006129.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 4265,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 18084,
"cdna_start": null,
"cds_end": null,
"cds_length": 12798,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 79,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017006130.2",
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"hgvs_c": "c.5094+3A>T",
"hgvs_p": null,
"intron_rank": 32,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861619.1",
"strand": true,
"transcript": "XM_017006130.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 4246,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 18027,
"cdna_start": null,
"cds_end": null,
"cds_length": 12741,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 79,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017006131.2",
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"hgvs_c": "c.5094+3A>T",
"hgvs_p": null,
"intron_rank": 32,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016861620.1",
"strand": true,
"transcript": "XM_017006131.2",
"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": 13300,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 77,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000486752.5",
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"hgvs_c": "n.5355+3A>T",
"hgvs_p": null,
"intron_rank": 31,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000486752.5",
"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": 223,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000466628.1",
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"hgvs_c": "n.*28A>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": "ENST00000466628.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs149183773",
"effect": "splice_region_variant,intron_variant",
"frequency_reference_population": 0.00064798247,
"gene_hgnc_id": 2940,
"gene_symbol": "DNAH1",
"gnomad_exomes_ac": 496,
"gnomad_exomes_af": 0.000339651,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_ac": 549,
"gnomad_genomes_af": 0.00360293,
"gnomad_genomes_homalt": 4,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 7,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Spermatogenic failure 18;Ciliary dyskinesia, primary, 37|DNAH1-related disorder|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.041,
"pos": 52362504,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.5600000023841858,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.56,
"transcript": "NM_015512.5"
}
]
}