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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: 17-40478583-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=40478583&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "TNS4",
"hgnc_id": 24352,
"hgvs_c": "c.1976G>A",
"hgvs_p": "p.Arg659Gln",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_032865.6",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 18,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.1971,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.19,
"chr": "17",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8418000340461731,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 715,
"aa_ref": "R",
"aa_start": 659,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4087,
"cdna_start": 2161,
"cds_end": null,
"cds_length": 2148,
"cds_start": 1976,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_032865.6",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "c.1976G>A",
"hgvs_p": "p.Arg659Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000254051.11",
"protein_coding": true,
"protein_id": "NP_116254.4",
"strand": false,
"transcript": "NM_032865.6",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 715,
"aa_ref": "R",
"aa_start": 659,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4087,
"cdna_start": 2161,
"cds_end": null,
"cds_length": 2148,
"cds_start": 1976,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000254051.11",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "c.1976G>A",
"hgvs_p": "p.Arg659Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_032865.6",
"protein_coding": true,
"protein_id": "ENSP00000254051.6",
"strand": false,
"transcript": "ENST00000254051.11",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2174,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000394072.7",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "n.242G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000394072.7",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 658,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4090,
"cdna_start": 2162,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1973,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000876606.1",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "c.1973G>A",
"hgvs_p": "p.Arg658Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546665.1",
"strand": false,
"transcript": "ENST00000876606.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 32,
"aa_ref": "R",
"aa_start": 22,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 599,
"cdna_start": 66,
"cds_end": null,
"cds_length": 99,
"cds_start": 65,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000582747.1",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "c.65G>A",
"hgvs_p": "p.Arg22Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000463456.1",
"strand": false,
"transcript": "ENST00000582747.1",
"transcript_support_level": 3
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 827,
"aa_ref": "R",
"aa_start": 771,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 2497,
"cds_end": null,
"cds_length": 2484,
"cds_start": 2312,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_047436949.1",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "c.2312G>A",
"hgvs_p": "p.Arg771Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047292905.1",
"strand": false,
"transcript": "XM_047436949.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 714,
"aa_ref": "R",
"aa_start": 658,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4084,
"cdna_start": 2158,
"cds_end": null,
"cds_length": 2145,
"cds_start": 1973,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_005257744.2",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "c.1973G>A",
"hgvs_p": "p.Arg658Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005257801.1",
"strand": false,
"transcript": "XM_005257744.2",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 689,
"aa_ref": "R",
"aa_start": 633,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4009,
"cdna_start": 2083,
"cds_end": null,
"cds_length": 2070,
"cds_start": 1898,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017025236.2",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "c.1898G>A",
"hgvs_p": "p.Arg633Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016880725.1",
"strand": false,
"transcript": "XM_017025236.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 510,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000497303.1",
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"hgvs_c": "n.405G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000497303.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs145753216",
"effect": "missense_variant",
"frequency_reference_population": 0.000011152389,
"gene_hgnc_id": 24352,
"gene_symbol": "TNS4",
"gnomad_exomes_ac": 17,
"gnomad_exomes_af": 0.0000116296,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000656935,
"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": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.861,
"pos": 40478583,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.496,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_032865.6"
}
]
}