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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: 6-116278715-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=116278715&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 7,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "TSPYL1",
"hgnc_id": 12382,
"hgvs_c": "c.1116C>T",
"hgvs_p": "p.Asp372Asp",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -5,
"transcript": "NM_003309.4",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DSE",
"hgnc_id": 21144,
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -4,
"transcript": "NM_001322937.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate,BP7",
"acmg_score": -5,
"allele_count_reference_population": 4,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"chr": "6",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7300000190734863,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 437,
"aa_ref": "D",
"aa_start": 372,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5073,
"cdna_start": 1216,
"cds_end": null,
"cds_length": 1314,
"cds_start": 1116,
"consequences": [
"synonymous_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_003309.4",
"gene_hgnc_id": 12382,
"gene_symbol": "TSPYL1",
"hgvs_c": "c.1116C>T",
"hgvs_p": "p.Asp372Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000368608.4",
"protein_coding": true,
"protein_id": "NP_003300.1",
"strand": false,
"transcript": "NM_003309.4",
"transcript_support_level": null
},
{
"aa_alt": "D",
"aa_end": null,
"aa_length": 437,
"aa_ref": "D",
"aa_start": 372,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5073,
"cdna_start": 1216,
"cds_end": null,
"cds_length": 1314,
"cds_start": 1116,
"consequences": [
"synonymous_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000368608.4",
"gene_hgnc_id": 12382,
"gene_symbol": "TSPYL1",
"hgvs_c": "c.1116C>T",
"hgvs_p": "p.Asp372Asp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003309.4",
"protein_coding": true,
"protein_id": "ENSP00000357597.4",
"strand": false,
"transcript": "ENST00000368608.4",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11181,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001322937.2",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309866.1",
"strand": true,
"transcript": "NM_001322937.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11093,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001322938.2",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309867.1",
"strand": true,
"transcript": "NM_001322938.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5163,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000891542.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000561601.1",
"strand": true,
"transcript": "ENST00000891542.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4661,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 8,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000891543.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-263+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000561602.1",
"strand": true,
"transcript": "ENST00000891543.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4499,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000891544.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000561603.1",
"strand": true,
"transcript": "ENST00000891544.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 958,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4986,
"cdna_start": null,
"cds_end": null,
"cds_length": 2877,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000950996.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-179+19748G>A",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621055.1",
"strand": true,
"transcript": "ENST00000950996.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 771,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11177,
"cdna_start": null,
"cds_end": null,
"cds_length": 2316,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001322940.2",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-611+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001309869.1",
"strand": true,
"transcript": "NM_001322940.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 625,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11082,
"cdna_start": null,
"cds_end": null,
"cds_length": 1878,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001374520.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-954+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361449.1",
"strand": true,
"transcript": "NM_001374520.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 613,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10733,
"cdna_start": null,
"cds_end": null,
"cds_length": 1842,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001374521.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-641+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361450.1",
"strand": true,
"transcript": "NM_001374521.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 317,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2319,
"cdna_start": null,
"cds_end": null,
"cds_length": 954,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001374522.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001361451.1",
"strand": true,
"transcript": "NM_001374522.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 228,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1631,
"cdna_start": null,
"cds_end": null,
"cds_length": 687,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000647244.1",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495184.1",
"strand": true,
"transcript": "ENST00000647244.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 143,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1130,
"cdna_start": null,
"cds_end": null,
"cds_length": 432,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000430252.6",
"gene_hgnc_id": 21144,
"gene_symbol": "DSE",
"hgvs_c": "c.-54+19748G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000397597.2",
"strand": true,
"transcript": "ENST00000430252.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5875,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000652202.1",
"gene_hgnc_id": 12382,
"gene_symbol": "TSPYL1",
"hgvs_c": "n.1116C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000498597.1",
"strand": false,
"transcript": "ENST00000652202.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1339620596",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0000024782319,
"gene_hgnc_id": 12382,
"gene_symbol": "TSPYL1",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000205216,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657125,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.885,
"pos": 116278715,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_003309.4"
}
]
}