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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: 7-73671083-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=73671083&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 73671083,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001077621.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"hgvs_c": "c.463C>T",
"hgvs_p": "p.Arg155Cys",
"transcript": "NM_001077621.2",
"protein_id": "NP_001071089.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 251,
"cds_start": 463,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000324941.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001077621.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"hgvs_c": "c.463C>T",
"hgvs_p": "p.Arg155Cys",
"transcript": "ENST00000324941.5",
"protein_id": "ENSP00000320416.4",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 251,
"cds_start": 463,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001077621.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324941.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"hgvs_c": "c.460C>T",
"hgvs_p": "p.Arg154Cys",
"transcript": "ENST00000965880.1",
"protein_id": "ENSP00000635939.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 250,
"cds_start": 460,
"cds_end": null,
"cds_length": 753,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965880.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"hgvs_c": "c.457C>T",
"hgvs_p": "p.Arg153Cys",
"transcript": "ENST00000903466.1",
"protein_id": "ENSP00000573525.1",
"transcript_support_level": null,
"aa_start": 153,
"aa_end": null,
"aa_length": 249,
"cds_start": 457,
"cds_end": null,
"cds_length": 750,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903466.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"hgvs_c": "c.208C>T",
"hgvs_p": "p.Arg70Cys",
"transcript": "ENST00000451519.1",
"protein_id": "ENSP00000413337.1",
"transcript_support_level": 5,
"aa_start": 70,
"aa_end": null,
"aa_length": 166,
"cds_start": 208,
"cds_end": null,
"cds_length": 501,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000451519.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"hgvs_c": "c.340C>T",
"hgvs_p": "p.Arg114Cys",
"transcript": "XM_017011779.2",
"protein_id": "XP_016867268.1",
"transcript_support_level": null,
"aa_start": 114,
"aa_end": null,
"aa_length": 210,
"cds_start": 340,
"cds_end": null,
"cds_length": 633,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017011779.2"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"hgvs_c": "c.235C>T",
"hgvs_p": "p.Arg79Cys",
"transcript": "XM_047419927.1",
"protein_id": "XP_047275883.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 175,
"cds_start": 235,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047419927.1"
}
],
"gene_symbol": "VPS37D",
"gene_hgnc_id": 18287,
"dbsnp": "rs782513824",
"frequency_reference_population": 0.000016758258,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000171356,
"gnomad_genomes_af": 0.0000131413,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8429484367370605,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.717,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8728,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.763,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,BP6",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001077621.2",
"gene_symbol": "VPS37D",
"hgnc_id": 18287,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.463C>T",
"hgvs_p": "p.Arg155Cys"
}
],
"clinvar_disease": "EBV-positive nodal T- and NK-cell lymphoma",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "EBV-positive nodal T- and NK-cell lymphoma",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}