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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: 15-31066093-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=31066093&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TRPM1",
"hgnc_id": 7146,
"hgvs_c": "c.824T>C",
"hgvs_p": "p.Leu275Pro",
"inheritance_mode": "AD,AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_001252020.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_score": 4,
"allele_count_reference_population": 3,
"alphamissense_prediction": null,
"alphamissense_score": 0.9614,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.26,
"chr": "15",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "Congenital stationary night blindness 1C",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8296267986297607,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1625,
"aa_ref": "L",
"aa_start": 258,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5787,
"cdna_start": 925,
"cds_end": null,
"cds_length": 4878,
"cds_start": 773,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001252024.2",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.773T>C",
"hgvs_p": "p.Leu258Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000256552.11",
"protein_coding": true,
"protein_id": "NP_001238953.1",
"strand": false,
"transcript": "NM_001252024.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1625,
"aa_ref": "L",
"aa_start": 258,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5787,
"cdna_start": 925,
"cds_end": null,
"cds_length": 4878,
"cds_start": 773,
"consequences": [
"missense_variant"
],
"exon_count": 28,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000256552.11",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.773T>C",
"hgvs_p": "p.Leu258Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001252024.2",
"protein_coding": true,
"protein_id": "ENSP00000256552.7",
"strand": false,
"transcript": "ENST00000256552.11",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1642,
"aa_ref": "L",
"aa_start": 275,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5887,
"cdna_start": 1025,
"cds_end": null,
"cds_length": 4929,
"cds_start": 824,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000558445.6",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.824T>C",
"hgvs_p": "p.Leu275Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452946.2",
"strand": false,
"transcript": "ENST00000558445.6",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1603,
"aa_ref": "L",
"aa_start": 236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5701,
"cdna_start": 839,
"cds_end": null,
"cds_length": 4812,
"cds_start": 707,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000397795.7",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.707T>C",
"hgvs_p": "p.Leu236Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000380897.2",
"strand": false,
"transcript": "ENST00000397795.7",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1526,
"aa_ref": "L",
"aa_start": 165,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4581,
"cdna_start": 494,
"cds_end": null,
"cds_length": 4581,
"cds_start": 494,
"consequences": [
"missense_variant"
],
"exon_count": 24,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000558768.5",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.494T>C",
"hgvs_p": "p.Leu165Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000453119.2",
"strand": false,
"transcript": "ENST00000558768.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4454,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000560801.5",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "n.494T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453644.2",
"strand": false,
"transcript": "ENST00000560801.5",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1642,
"aa_ref": "L",
"aa_start": 275,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5887,
"cdna_start": 1025,
"cds_end": null,
"cds_length": 4929,
"cds_start": 824,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001252020.2",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.824T>C",
"hgvs_p": "p.Leu275Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001238949.1",
"strand": false,
"transcript": "NM_001252020.2",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1609,
"aa_ref": "L",
"aa_start": 236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5719,
"cdna_start": 839,
"cds_end": null,
"cds_length": 4830,
"cds_start": 707,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000711434.1",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.707T>C",
"hgvs_p": "p.Leu236Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000518752.1",
"strand": false,
"transcript": "ENST00000711434.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1603,
"aa_ref": "L",
"aa_start": 236,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5701,
"cdna_start": 839,
"cds_end": null,
"cds_length": 4812,
"cds_start": 707,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_002420.6",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.707T>C",
"hgvs_p": "p.Leu236Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_002411.3",
"strand": false,
"transcript": "NM_002420.6",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 757,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2274,
"cdna_start": null,
"cds_end": null,
"cds_length": 2274,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000559177.6",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "c.544+1786T>C",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000453477.2",
"strand": false,
"transcript": "ENST00000559177.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1649,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000560658.5",
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"hgvs_c": "n.707T>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454077.1",
"strand": false,
"transcript": "ENST00000560658.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs869312176",
"effect": "missense_variant",
"frequency_reference_population": 0.0000020523037,
"gene_hgnc_id": 7146,
"gene_symbol": "TRPM1",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.0000020523,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely pathogenic",
"phenotype_combined": "Congenital stationary night blindness 1C",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.312,
"pos": 31066093,
"ref": "A",
"revel_prediction": "Pathogenic",
"revel_score": 0.707,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001252020.2"
}
]
}