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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-115622404-GT-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=115622404&ref=GT&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 115622404,
"ref": "GT",
"alt": "G",
"effect": "frameshift_variant,splice_region_variant",
"transcript": "ENST00000355899.8",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "NM_005032.7",
"protein_id": "NP_005023.2",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 330,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": "ENST00000355899.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "ENST00000355899.8",
"protein_id": "ENSP00000348163.3",
"transcript_support_level": 1,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 330,
"cdna_end": null,
"cdna_length": 3288,
"mane_select": "NM_005032.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "ENST00000539310.5",
"protein_id": "ENSP00000445339.2",
"transcript_support_level": 1,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 3037,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "n.*488delT",
"hgvs_p": null,
"transcript": "ENST00000489283.5",
"protein_id": "ENSP00000420458.1",
"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": 926,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "n.*488delT",
"hgvs_p": null,
"transcript": "ENST00000489283.5",
"protein_id": "ENSP00000420458.1",
"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": 926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "NM_001136025.5",
"protein_id": "NP_001129497.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 325,
"cdna_end": null,
"cdna_length": 3283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "NM_001440791.1",
"protein_id": "NP_001427720.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 400,
"cdna_end": null,
"cdna_length": 3358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "NM_001440792.1",
"protein_id": "NP_001427721.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 427,
"cdna_end": null,
"cdna_length": 3385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.169delT",
"hgvs_p": "p.Tyr57fs",
"transcript": "NM_001282337.2",
"protein_id": "NP_001269266.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 617,
"cds_start": 169,
"cds_end": null,
"cds_length": 1854,
"cdna_start": 449,
"cdna_end": null,
"cdna_length": 3434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.169delT",
"hgvs_p": "p.Tyr57fs",
"transcript": "ENST00000289290.7",
"protein_id": "ENSP00000289290.4",
"transcript_support_level": 2,
"aa_start": 57,
"aa_end": null,
"aa_length": 617,
"cds_start": 169,
"cds_end": null,
"cds_length": 1854,
"cdna_start": 395,
"cdna_end": null,
"cdna_length": 2277,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.100delT",
"hgvs_p": "p.Tyr34fs",
"transcript": "NM_001282338.2",
"protein_id": "NP_001269267.1",
"transcript_support_level": null,
"aa_start": 34,
"aa_end": null,
"aa_length": 585,
"cds_start": 100,
"cds_end": null,
"cds_length": 1758,
"cdna_start": 707,
"cdna_end": null,
"cdna_length": 3665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "ENST00000473026.6",
"protein_id": "ENSP00000475900.1",
"transcript_support_level": 3,
"aa_start": 79,
"aa_end": null,
"aa_length": 163,
"cds_start": 235,
"cds_end": null,
"cds_length": 492,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 500,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "XM_047442168.1",
"protein_id": "XP_047298124.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 502,
"cdna_end": null,
"cdna_length": 3460,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "XM_047442169.1",
"protein_id": "XP_047298125.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 523,
"cdna_end": null,
"cdna_length": 3481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "XM_047442171.1",
"protein_id": "XP_047298127.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 2578,
"cdna_end": null,
"cdna_length": 5536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs",
"transcript": "XM_047442172.1",
"protein_id": "XP_047298128.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 630,
"cds_start": 235,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 2653,
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "n.*488delT",
"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": 4,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "n.*488delT",
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"hgvs_c": "c.156+79delT",
"hgvs_p": null,
"transcript": "NM_001172335.3",
"protein_id": "NP_001165806.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 603,
"cds_start": -4,
"cds_end": null,
"cds_length": 1812,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3202,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLS3",
"gene_hgnc_id": 9091,
"dbsnp": "rs397518463",
"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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 6.271,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": [
"frameshift_variant",
"splice_region_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.235delT",
"hgvs_p": "p.Tyr79fs"
}
],
"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
}