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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: 9-95453491-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=95453491&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 95453491,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000331920.11",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3436G>A",
"hgvs_p": "p.Asp1146Asn",
"transcript": "NM_000264.5",
"protein_id": "NP_000255.2",
"transcript_support_level": null,
"aa_start": 1146,
"aa_end": null,
"aa_length": 1447,
"cds_start": 3436,
"cds_end": null,
"cds_length": 4344,
"cdna_start": 4341,
"cdna_end": null,
"cdna_length": 8662,
"mane_select": "ENST00000331920.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3436G>A",
"hgvs_p": "p.Asp1146Asn",
"transcript": "ENST00000331920.11",
"protein_id": "ENSP00000332353.6",
"transcript_support_level": 5,
"aa_start": 1146,
"aa_end": null,
"aa_length": 1447,
"cds_start": 3436,
"cds_end": null,
"cds_length": 4344,
"cdna_start": 4341,
"cdna_end": null,
"cdna_length": 8662,
"mane_select": "NM_000264.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3433G>A",
"hgvs_p": "p.Asp1145Asn",
"transcript": "NM_001083603.3",
"protein_id": "NP_001077072.1",
"transcript_support_level": null,
"aa_start": 1145,
"aa_end": null,
"aa_length": 1446,
"cds_start": 3433,
"cds_end": null,
"cds_length": 4341,
"cdna_start": 3584,
"cdna_end": null,
"cdna_length": 7905,
"mane_select": null,
"mane_plus": "ENST00000437951.6",
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3433G>A",
"hgvs_p": "p.Asp1145Asn",
"transcript": "ENST00000437951.6",
"protein_id": "ENSP00000389744.2",
"transcript_support_level": 5,
"aa_start": 1145,
"aa_end": null,
"aa_length": 1446,
"cds_start": 3433,
"cds_end": null,
"cds_length": 4341,
"cdna_start": 3584,
"cdna_end": null,
"cdna_length": 7905,
"mane_select": null,
"mane_plus": "NM_001083603.3",
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.2983G>A",
"hgvs_p": "p.Asp995Asn",
"transcript": "ENST00000429896.6",
"protein_id": "ENSP00000414823.2",
"transcript_support_level": 1,
"aa_start": 995,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2983,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 3424,
"cdna_end": null,
"cdna_length": 6563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3280G>A",
"hgvs_p": "p.Asp1094Asn",
"transcript": "NM_001354918.2",
"protein_id": "NP_001341847.1",
"transcript_support_level": null,
"aa_start": 1094,
"aa_end": null,
"aa_length": 1395,
"cds_start": 3280,
"cds_end": null,
"cds_length": 4188,
"cdna_start": 4185,
"cdna_end": null,
"cdna_length": 8506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3238G>A",
"hgvs_p": "p.Asp1080Asn",
"transcript": "NM_001083602.3",
"protein_id": "NP_001077071.1",
"transcript_support_level": null,
"aa_start": 1080,
"aa_end": null,
"aa_length": 1381,
"cds_start": 3238,
"cds_end": null,
"cds_length": 4146,
"cdna_start": 3738,
"cdna_end": null,
"cdna_length": 8059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3238G>A",
"hgvs_p": "p.Asp1080Asn",
"transcript": "ENST00000430669.6",
"protein_id": "ENSP00000410287.2",
"transcript_support_level": 5,
"aa_start": 1080,
"aa_end": null,
"aa_length": 1381,
"cds_start": 3238,
"cds_end": null,
"cds_length": 4146,
"cdna_start": 3824,
"cdna_end": null,
"cdna_length": 8232,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.3238G>A",
"hgvs_p": "p.Asp1080Asn",
"transcript": "ENST00000711046.1",
"protein_id": "ENSP00000518556.1",
"transcript_support_level": null,
"aa_start": 1080,
"aa_end": null,
"aa_length": 1381,
"cds_start": 3238,
"cds_end": null,
"cds_length": 4146,
"cdna_start": 3738,
"cdna_end": null,
"cdna_length": 8059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.2983G>A",
"hgvs_p": "p.Asp995Asn",
"transcript": "NM_001083604.3",
"protein_id": "NP_001077073.1",
"transcript_support_level": null,
"aa_start": 995,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2983,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 3342,
"cdna_end": null,
"cdna_length": 7663,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.2983G>A",
"hgvs_p": "p.Asp995Asn",
"transcript": "NM_001083605.3",
"protein_id": "NP_001077074.1",
"transcript_support_level": null,
"aa_start": 995,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2983,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 3325,
"cdna_end": null,
"cdna_length": 7646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.2983G>A",
"hgvs_p": "p.Asp995Asn",
"transcript": "NM_001083606.3",
"protein_id": "NP_001077075.1",
"transcript_support_level": null,
"aa_start": 995,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2983,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 3434,
"cdna_end": null,
"cdna_length": 7755,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.2983G>A",
"hgvs_p": "p.Asp995Asn",
"transcript": "NM_001083607.3",
"protein_id": "NP_001077076.1",
"transcript_support_level": null,
"aa_start": 995,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2983,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 3498,
"cdna_end": null,
"cdna_length": 7819,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "c.2983G>A",
"hgvs_p": "p.Asp995Asn",
"transcript": "ENST00000692981.1",
"protein_id": "ENSP00000510238.1",
"transcript_support_level": null,
"aa_start": 995,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2983,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 3124,
"cdna_end": null,
"cdna_length": 7000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.*1744G>A",
"hgvs_p": null,
"transcript": "ENST00000375290.6",
"protein_id": "ENSP00000364439.2",
"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": 10631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.*1744G>A",
"hgvs_p": null,
"transcript": "ENST00000690194.1",
"protein_id": "ENSP00000509379.1",
"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": 7135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.767G>A",
"hgvs_p": null,
"transcript": "ENST00000693534.1",
"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": 4653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.4175G>A",
"hgvs_p": null,
"transcript": "NR_149061.2",
"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": 8496,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.*1744G>A",
"hgvs_p": null,
"transcript": "ENST00000375290.6",
"protein_id": "ENSP00000364439.2",
"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": 10631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"hgvs_c": "n.*1744G>A",
"hgvs_p": null,
"transcript": "ENST00000690194.1",
"protein_id": "ENSP00000509379.1",
"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": 7135,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTCH1",
"gene_hgnc_id": 9585,
"dbsnp": "rs749542089",
"frequency_reference_population": 0.000009913492,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.00000752511,
"gnomad_genomes_af": 0.0000328537,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7726007103919983,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.707,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8119,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.388,
"phylop100way_prediction": "Uncertain_significance",
"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": "PP3,BP6,BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000331920.11",
"gene_symbol": "PTCH1",
"hgnc_id": 9585,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3436G>A",
"hgvs_p": "p.Asp1146Asn"
}
],
"clinvar_disease": " 1, susceptibility to,Basal cell carcinoma,Gorlin syndrome,Hereditary cancer-predisposing syndrome,Holoprosencephaly 7",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 B:1",
"phenotype_combined": "Gorlin syndrome|Hereditary cancer-predisposing syndrome|Holoprosencephaly 7;Gorlin syndrome;Basal cell carcinoma, susceptibility to, 1",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}