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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-153737159-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153737159&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153737159,
"ref": "C",
"alt": "T",
"effect": "stop_gained,splice_region_variant",
"transcript": "NM_001440747.1",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1396C>T",
"hgvs_p": "p.Gln466*",
"transcript": "NM_000033.4",
"protein_id": "NP_000024.2",
"transcript_support_level": null,
"aa_start": 466,
"aa_end": null,
"aa_length": 745,
"cds_start": 1396,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000218104.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000033.4"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1396C>T",
"hgvs_p": "p.Gln466*",
"transcript": "ENST00000218104.6",
"protein_id": "ENSP00000218104.3",
"transcript_support_level": 1,
"aa_start": 466,
"aa_end": null,
"aa_length": 745,
"cds_start": 1396,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000033.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000218104.6"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1696C>T",
"hgvs_p": "p.Gln566*",
"transcript": "NM_001440747.1",
"protein_id": "NP_001427676.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 845,
"cds_start": 1696,
"cds_end": null,
"cds_length": 2538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001440747.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1696C>T",
"hgvs_p": "p.Gln566*",
"transcript": "ENST00000862307.1",
"protein_id": "ENSP00000532366.1",
"transcript_support_level": null,
"aa_start": 566,
"aa_end": null,
"aa_length": 845,
"cds_start": 1696,
"cds_end": null,
"cds_length": 2538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862307.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1666C>T",
"hgvs_p": "p.Gln556*",
"transcript": "ENST00000862306.1",
"protein_id": "ENSP00000532365.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 835,
"cds_start": 1666,
"cds_end": null,
"cds_length": 2508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000862306.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1489C>T",
"hgvs_p": "p.Gln497*",
"transcript": "ENST00000935199.1",
"protein_id": "ENSP00000605258.1",
"transcript_support_level": null,
"aa_start": 497,
"aa_end": null,
"aa_length": 776,
"cds_start": 1489,
"cds_end": null,
"cds_length": 2331,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935199.1"
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1390C>T",
"hgvs_p": "p.Gln464*",
"transcript": "ENST00000968902.1",
"protein_id": "ENSP00000638961.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 743,
"cds_start": 1390,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968902.1"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "c.1452C>T",
"hgvs_p": "p.Ala484Ala",
"transcript": "XM_047441917.1",
"protein_id": "XP_047297873.1",
"transcript_support_level": null,
"aa_start": 484,
"aa_end": null,
"aa_length": 575,
"cds_start": 1452,
"cds_end": null,
"cds_length": 1728,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441917.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"hgvs_c": "n.399C>T",
"hgvs_p": null,
"transcript": "ENST00000443684.2",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000443684.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.1509G>A",
"hgvs_p": null,
"transcript": "NR_199693.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_199693.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.1617G>A",
"hgvs_p": null,
"transcript": "NR_199694.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_199694.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.1728G>A",
"hgvs_p": null,
"transcript": "NR_199695.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_199695.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.1649G>A",
"hgvs_p": null,
"transcript": "NR_199696.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_199696.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "PLXNB3-AS1",
"gene_hgnc_id": 40454,
"hgvs_c": "n.580+911G>A",
"hgvs_p": null,
"transcript": "ENST00000434284.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000434284.1"
}
],
"gene_symbol": "ABCD1",
"gene_hgnc_id": 61,
"dbsnp": "rs398123100",
"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": 0.5600000023841858,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.56,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.282,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_001440747.1",
"gene_symbol": "ABCD1",
"hgnc_id": 61,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.1696C>T",
"hgvs_p": "p.Gln566*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NR_199693.1",
"gene_symbol": "PLXNB3-AS1",
"hgnc_id": 40454,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1509G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Adrenoleukodystrophy,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "not provided|Adrenoleukodystrophy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}