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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: 2-208443391-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=208443391&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 208443391,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000272847.7",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Met",
"transcript": "NM_005048.4",
"protein_id": "NP_005039.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 550,
"cds_start": 553,
"cds_end": null,
"cds_length": 1653,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 2752,
"mane_select": "ENST00000272847.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Met",
"transcript": "ENST00000272847.7",
"protein_id": "ENSP00000272847.2",
"transcript_support_level": 1,
"aa_start": 185,
"aa_end": null,
"aa_length": 550,
"cds_start": 553,
"cds_end": null,
"cds_length": 1653,
"cdna_start": 805,
"cdna_end": null,
"cdna_length": 2752,
"mane_select": "NM_005048.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Val74Met",
"transcript": "NM_001309516.2",
"protein_id": "NP_001296445.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 439,
"cds_start": 220,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1024,
"cdna_end": null,
"cdna_length": 2971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Val74Met",
"transcript": "NM_001371905.1",
"protein_id": "NP_001358834.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 439,
"cds_start": 220,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1091,
"cdna_end": null,
"cdna_length": 3038,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Val74Met",
"transcript": "NM_001371906.1",
"protein_id": "NP_001358835.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 439,
"cds_start": 220,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1100,
"cdna_end": null,
"cdna_length": 3047,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Val74Met",
"transcript": "ENST00000617735.4",
"protein_id": "ENSP00000482485.1",
"transcript_support_level": 2,
"aa_start": 74,
"aa_end": null,
"aa_length": 439,
"cds_start": 220,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 2472,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "c.220G>A",
"hgvs_p": "p.Val74Met",
"transcript": "NM_001371907.1",
"protein_id": "NP_001358836.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 347,
"cds_start": 220,
"cds_end": null,
"cds_length": 1044,
"cdna_start": 1024,
"cdna_end": null,
"cdna_length": 2695,
"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": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "n.1024G>A",
"hgvs_p": null,
"transcript": "NR_163991.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2876,
"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": 6,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "n.1024G>A",
"hgvs_p": null,
"transcript": "NR_163993.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3076,
"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": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "n.1024G>A",
"hgvs_p": null,
"transcript": "NR_163994.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3104,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"hgvs_c": "n.981-19G>A",
"hgvs_p": null,
"transcript": "NR_163992.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTH2R",
"gene_hgnc_id": 9609,
"dbsnp": "rs149297616",
"frequency_reference_population": 0.000329803,
"hom_count_reference_population": 0,
"allele_count_reference_population": 531,
"gnomad_exomes_af": 0.000324459,
"gnomad_genomes_af": 0.000380972,
"gnomad_exomes_ac": 473,
"gnomad_genomes_ac": 58,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.016200095415115356,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.075,
"revel_prediction": "Benign",
"alphamissense_score": 0.1155,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.687,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000272847.7",
"gene_symbol": "PTH2R",
"hgnc_id": 9609,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.553G>A",
"hgvs_p": "p.Val185Met"
}
],
"clinvar_disease": "PTH2R-related disorder,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "PTH2R-related disorder|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}