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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-115646495-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=115646495&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 115646495,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000355899.8",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "NM_005032.7",
"protein_id": "NP_005023.2",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1566,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": "ENST00000355899.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "ENST00000355899.8",
"protein_id": "ENSP00000348163.3",
"transcript_support_level": 1,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1566,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": "NM_005032.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "ENST00000539310.5",
"protein_id": "ENSP00000445339.2",
"transcript_support_level": 1,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1504,
"cdna_end": null,
"cdna_length": 3037,
"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"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "NM_001136025.5",
"protein_id": "NP_001129497.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1561,
"cdna_end": null,
"cdna_length": 3283,
"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"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "NM_001440791.1",
"protein_id": "NP_001427720.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1636,
"cdna_end": null,
"cdna_length": 3358,
"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"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "NM_001440792.1",
"protein_id": "NP_001427721.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1663,
"cdna_end": null,
"cdna_length": 3385,
"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"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1432C>T",
"hgvs_p": "p.Gln478*",
"transcript": "NM_001282337.2",
"protein_id": "NP_001269266.1",
"transcript_support_level": null,
"aa_start": 478,
"aa_end": null,
"aa_length": 617,
"cds_start": 1432,
"cds_end": null,
"cds_length": 1854,
"cdna_start": 1712,
"cdna_end": null,
"cdna_length": 3434,
"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"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1432C>T",
"hgvs_p": "p.Gln478*",
"transcript": "ENST00000289290.7",
"protein_id": "ENSP00000289290.4",
"transcript_support_level": 2,
"aa_start": 478,
"aa_end": null,
"aa_length": 617,
"cds_start": 1432,
"cds_end": null,
"cds_length": 1854,
"cdna_start": 1658,
"cdna_end": null,
"cdna_length": 2277,
"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"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1390C>T",
"hgvs_p": "p.Gln464*",
"transcript": "NM_001172335.3",
"protein_id": "NP_001165806.1",
"transcript_support_level": null,
"aa_start": 464,
"aa_end": null,
"aa_length": 603,
"cds_start": 1390,
"cds_end": null,
"cds_length": 1812,
"cdna_start": 1480,
"cdna_end": null,
"cdna_length": 3202,
"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"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1336C>T",
"hgvs_p": "p.Gln446*",
"transcript": "NM_001282338.2",
"protein_id": "NP_001269267.1",
"transcript_support_level": null,
"aa_start": 446,
"aa_end": null,
"aa_length": 585,
"cds_start": 1336,
"cds_end": null,
"cds_length": 1758,
"cdna_start": 1943,
"cdna_end": null,
"cdna_length": 3665,
"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"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "XM_047442168.1",
"protein_id": "XP_047298124.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1738,
"cdna_end": null,
"cdna_length": 3460,
"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"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "XM_047442169.1",
"protein_id": "XP_047298125.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1759,
"cdna_end": null,
"cdna_length": 3481,
"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"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "XM_047442171.1",
"protein_id": "XP_047298127.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 3814,
"cdna_end": null,
"cdna_length": 5536,
"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"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*",
"transcript": "XM_047442172.1",
"protein_id": "XP_047298128.1",
"transcript_support_level": null,
"aa_start": 491,
"aa_end": null,
"aa_length": 630,
"cds_start": 1471,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 3889,
"cdna_end": null,
"cdna_length": 5611,
"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": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "n.*1724C>T",
"hgvs_p": null,
"transcript": "ENST00000481823.5",
"protein_id": "ENSP00000419051.1",
"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": 2858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "n.*1724C>T",
"hgvs_p": null,
"transcript": "ENST00000481823.5",
"protein_id": "ENSP00000419051.1",
"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": 2858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.*64C>T",
"hgvs_p": null,
"transcript": "ENST00000497870.1",
"protein_id": "ENSP00000417728.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 188,
"cds_start": -4,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"dbsnp": "rs397518421",
"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,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.252,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "ENST00000355899.8",
"gene_symbol": "PLS3",
"hgnc_id": 9091,
"effects": [
"stop_gained"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1471C>T",
"hgvs_p": "p.Gln491*"
}
],
"clinvar_disease": "Bone mineral density quantitative trait locus 18",
"clinvar_classification": "association",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Bone mineral density quantitative trait locus 18",
"pathogenicity_classification_combined": "association",
"custom_annotations": null
}
],
"message": null
}