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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: X-48684421-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=48684421&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 48684421,
"ref": "C",
"alt": "T",
"effect": "stop_gained,splice_region_variant",
"transcript": "ENST00000376701.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "NM_000377.3",
"protein_id": "NP_000368.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 502,
"cds_start": 271,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 326,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": "ENST00000376701.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "ENST00000376701.5",
"protein_id": "ENSP00000365891.4",
"transcript_support_level": 1,
"aa_start": 91,
"aa_end": null,
"aa_length": 502,
"cds_start": 271,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 326,
"cdna_end": null,
"cdna_length": 1829,
"mane_select": "NM_000377.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "NM_001438877.1",
"protein_id": "NP_001425806.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 590,
"cds_start": 271,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 326,
"cdna_end": null,
"cdna_length": 2786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "ENST00000698635.1",
"protein_id": "ENSP00000513850.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 590,
"cds_start": 271,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 320,
"cdna_end": null,
"cdna_length": 2761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "NM_001438878.1",
"protein_id": "NP_001425807.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 538,
"cds_start": 271,
"cds_end": null,
"cds_length": 1617,
"cdna_start": 326,
"cdna_end": null,
"cdna_length": 2630,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "ENST00000698626.1",
"protein_id": "ENSP00000513845.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 532,
"cds_start": 271,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 1886,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "NM_001438879.1",
"protein_id": "NP_001425808.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 502,
"cds_start": 271,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 1921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "ENST00000698625.1",
"protein_id": "ENSP00000513844.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 502,
"cds_start": 271,
"cds_end": null,
"cds_length": 1509,
"cdna_start": 450,
"cdna_end": null,
"cdna_length": 1957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "NM_001438876.1",
"protein_id": "NP_001425805.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 450,
"cds_start": 271,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 326,
"cdna_end": null,
"cdna_length": 1673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "ENST00000450772.5",
"protein_id": "ENSP00000410537.1",
"transcript_support_level": 3,
"aa_start": 91,
"aa_end": null,
"aa_length": 215,
"cds_start": 271,
"cds_end": null,
"cds_length": 650,
"cdna_start": 554,
"cdna_end": null,
"cdna_length": 933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "XM_017029786.2",
"protein_id": "XP_016885275.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 590,
"cds_start": 271,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 2878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "XM_047442432.1",
"protein_id": "XP_047298388.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 590,
"cds_start": 271,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 344,
"cdna_end": null,
"cdna_length": 2804,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "XM_047442433.1",
"protein_id": "XP_047298389.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 538,
"cds_start": 271,
"cds_end": null,
"cds_length": 1617,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 2722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*",
"transcript": "XM_011543977.3",
"protein_id": "XP_011542279.1",
"transcript_support_level": null,
"aa_start": 91,
"aa_end": null,
"aa_length": 450,
"cds_start": 271,
"cds_end": null,
"cds_length": 1353,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 1765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"hgvs_c": "n.304C>T",
"hgvs_p": null,
"transcript": "ENST00000483750.6",
"protein_id": null,
"transcript_support_level": 5,
"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": 1100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000232828",
"gene_hgnc_id": null,
"hgvs_c": "n.821+14603G>A",
"hgvs_p": null,
"transcript": "ENST00000746890.1",
"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": 1256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WAS",
"gene_hgnc_id": 12731,
"dbsnp": "rs1557006354",
"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": 0.6000000238418579,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9020000100135803,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.294,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.998238609009033,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 13,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 13,
"benign_score": 0,
"pathogenic_score": 13,
"criteria": [
"PVS1",
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000376701.5",
"gene_symbol": "WAS",
"hgnc_id": 12731,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.271C>T",
"hgvs_p": "p.Gln91*"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000746890.1",
"gene_symbol": "ENSG00000232828",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.821+14603G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Thrombocytopenia 1,Wiskott-Aldrich syndrome,X-linked severe congenital neutropenia",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Thrombocytopenia 1;Wiskott-Aldrich syndrome;X-linked severe congenital neutropenia",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}