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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: 11-6390607-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=6390607&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 6390607,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000543.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg",
"transcript": "NM_000543.5",
"protein_id": "NP_000534.3",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 631,
"cds_start": 9,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 134,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": "ENST00000342245.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg",
"transcript": "ENST00000342245.9",
"protein_id": "ENSP00000340409.4",
"transcript_support_level": 1,
"aa_start": 3,
"aa_end": null,
"aa_length": 631,
"cds_start": 9,
"cds_end": null,
"cds_length": 1896,
"cdna_start": 134,
"cdna_end": null,
"cdna_length": 2410,
"mane_select": "NM_000543.5",
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.9C>T",
"hgvs_p": null,
"transcript": "ENST00000531303.5",
"protein_id": "ENSP00000432625.1",
"transcript_support_level": 1,
"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": 1451,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.9C>T",
"hgvs_p": null,
"transcript": "ENST00000533123.5",
"protein_id": "ENSP00000435950.1",
"transcript_support_level": 1,
"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": 2211,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.9C>T",
"hgvs_p": null,
"transcript": "ENST00000534405.5",
"protein_id": "ENSP00000434353.1",
"transcript_support_level": 1,
"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": 2446,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg",
"transcript": "NM_001007593.3",
"protein_id": "NP_001007594.2",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 630,
"cds_start": 9,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 134,
"cdna_end": null,
"cdna_length": 2407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg",
"transcript": "ENST00000527275.5",
"protein_id": "ENSP00000435350.1",
"transcript_support_level": 2,
"aa_start": 3,
"aa_end": null,
"aa_length": 630,
"cds_start": 9,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 133,
"cdna_end": null,
"cdna_length": 2188,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg",
"transcript": "NM_001365135.2",
"protein_id": "NP_001352064.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 587,
"cds_start": 9,
"cds_end": null,
"cds_length": 1764,
"cdna_start": 134,
"cdna_end": null,
"cdna_length": 2278,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg",
"transcript": "NM_001318087.2",
"protein_id": "NP_001305016.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 508,
"cds_start": 9,
"cds_end": null,
"cds_length": 1527,
"cdna_start": 134,
"cdna_end": null,
"cdna_length": 2430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg",
"transcript": "XM_011520304.3",
"protein_id": "XP_011518606.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 464,
"cds_start": 9,
"cds_end": null,
"cds_length": 1395,
"cdna_start": 134,
"cdna_end": null,
"cdna_length": 2298,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.168C>T",
"hgvs_p": null,
"transcript": "ENST00000533196.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 425,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.134C>T",
"hgvs_p": null,
"transcript": "NR_027400.3",
"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": 2238,
"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": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "n.134C>T",
"hgvs_p": null,
"transcript": "NR_134502.2",
"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": 1777,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.-953C>T",
"hgvs_p": null,
"transcript": "NM_001318088.2",
"protein_id": "NP_001305017.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 324,
"cds_start": -4,
"cds_end": null,
"cds_length": 975,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"hgvs_c": "c.-128C>T",
"hgvs_p": null,
"transcript": "ENST00000530395.1",
"protein_id": "ENSP00000431479.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 51,
"cds_start": -4,
"cds_end": null,
"cds_length": 158,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 447,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SMPD1",
"gene_hgnc_id": 11120,
"dbsnp": "rs2134004441",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5899999737739563,
"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": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.149,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 7,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_000543.5",
"gene_symbol": "SMPD1",
"hgnc_id": 11120,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.9C>T",
"hgvs_p": "p.Arg3Arg"
}
],
"clinvar_disease": " type A, type B,Niemann-Pick disease",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Niemann-Pick disease, type A;Niemann-Pick disease, type B",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}