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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: 3-52392973-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=52392973&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 52392973,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000420323.7",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 78,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "c.10422T>C",
"hgvs_p": "p.Leu3474Leu",
"transcript": "NM_015512.5",
"protein_id": "NP_056327.4",
"transcript_support_level": null,
"aa_start": 3474,
"aa_end": null,
"aa_length": 4265,
"cds_start": 10422,
"cds_end": null,
"cds_length": 12798,
"cdna_start": 10683,
"cdna_end": null,
"cdna_length": 13105,
"mane_select": "ENST00000420323.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 65,
"exon_rank_end": null,
"exon_count": 78,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "c.10422T>C",
"hgvs_p": "p.Leu3474Leu",
"transcript": "ENST00000420323.7",
"protein_id": "ENSP00000401514.2",
"transcript_support_level": 1,
"aa_start": 3474,
"aa_end": null,
"aa_length": 4265,
"cds_start": 10422,
"cds_end": null,
"cds_length": 12798,
"cdna_start": 10683,
"cdna_end": null,
"cdna_length": 13105,
"mane_select": "NM_015512.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 67,
"exon_rank_end": null,
"exon_count": 80,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "c.10491T>C",
"hgvs_p": "p.Leu3497Leu",
"transcript": "XM_017006129.2",
"protein_id": "XP_016861618.1",
"transcript_support_level": null,
"aa_start": 3497,
"aa_end": null,
"aa_length": 4288,
"cds_start": 10491,
"cds_end": null,
"cds_length": 12867,
"cdna_start": 15731,
"cdna_end": null,
"cdna_length": 18153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 66,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "c.10422T>C",
"hgvs_p": "p.Leu3474Leu",
"transcript": "XM_017006130.2",
"protein_id": "XP_016861619.1",
"transcript_support_level": null,
"aa_start": 3474,
"aa_end": null,
"aa_length": 4265,
"cds_start": 10422,
"cds_end": null,
"cds_length": 12798,
"cdna_start": 15662,
"cdna_end": null,
"cdna_length": 18084,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 66,
"exon_rank_end": null,
"exon_count": 79,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "c.10365T>C",
"hgvs_p": "p.Leu3455Leu",
"transcript": "XM_017006131.2",
"protein_id": "XP_016861620.1",
"transcript_support_level": null,
"aa_start": 3455,
"aa_end": null,
"aa_length": 4246,
"cds_start": 10365,
"cds_end": null,
"cds_length": 12741,
"cdna_start": 15605,
"cdna_end": null,
"cdna_length": 18027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 64,
"exon_rank_end": null,
"exon_count": 77,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "n.10879T>C",
"hgvs_p": null,
"transcript": "ENST00000486752.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 13300,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "n.2208T>C",
"hgvs_p": null,
"transcript": "ENST00000488988.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 4549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"hgvs_c": "n.1122T>C",
"hgvs_p": null,
"transcript": "ENST00000490713.5",
"protein_id": "ENSP00000419071.1",
"transcript_support_level": 5,
"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": 3408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAH1",
"gene_hgnc_id": 2940,
"dbsnp": "rs148913561",
"frequency_reference_population": 0.0055941637,
"hom_count_reference_population": 69,
"allele_count_reference_population": 9027,
"gnomad_exomes_af": 0.00578657,
"gnomad_genomes_af": 0.00374377,
"gnomad_exomes_ac": 8458,
"gnomad_genomes_ac": 569,
"gnomad_exomes_homalt": 65,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6100000143051147,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.61,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.403,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000420323.7",
"gene_symbol": "DNAH1",
"hgnc_id": 2940,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.10422T>C",
"hgvs_p": "p.Leu3474Leu"
}
],
"clinvar_disease": " 37, primary,Ciliary dyskinesia,Spermatogenic failure 18,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:2",
"phenotype_combined": "Spermatogenic failure 18;Ciliary dyskinesia, primary, 37|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}