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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: 3-41883931-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=41883931&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 41883931,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000301831.9",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.1599A>G",
"hgvs_p": "p.Val533Val",
"transcript": "NM_017886.4",
"protein_id": "NP_060356.2",
"transcript_support_level": null,
"aa_start": 533,
"aa_end": null,
"aa_length": 1275,
"cds_start": 1599,
"cds_end": null,
"cds_length": 3828,
"cdna_start": 1735,
"cdna_end": null,
"cdna_length": 4294,
"mane_select": "ENST00000301831.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.1599A>G",
"hgvs_p": "p.Val533Val",
"transcript": "ENST00000301831.9",
"protein_id": "ENSP00000301831.4",
"transcript_support_level": 2,
"aa_start": 533,
"aa_end": null,
"aa_length": 1275,
"cds_start": 1599,
"cds_end": null,
"cds_length": 3828,
"cdna_start": 1735,
"cdna_end": null,
"cdna_length": 4294,
"mane_select": "NM_017886.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.1599A>G",
"hgvs_p": "p.Val533Val",
"transcript": "ENST00000420927.5",
"protein_id": "ENSP00000412187.1",
"transcript_support_level": 1,
"aa_start": 533,
"aa_end": null,
"aa_length": 580,
"cds_start": 1599,
"cds_end": null,
"cds_length": 1743,
"cdna_start": 1716,
"cdna_end": null,
"cdna_length": 1904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.1599A>G",
"hgvs_p": "p.Val533Val",
"transcript": "NM_001322500.2",
"protein_id": "NP_001309429.1",
"transcript_support_level": null,
"aa_start": 533,
"aa_end": null,
"aa_length": 1235,
"cds_start": 1599,
"cds_end": null,
"cds_length": 3708,
"cdna_start": 1735,
"cdna_end": null,
"cdna_length": 4323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "c.693A>G",
"hgvs_p": "p.Val231Val",
"transcript": "NM_001322501.2",
"protein_id": "NP_001309430.1",
"transcript_support_level": null,
"aa_start": 231,
"aa_end": null,
"aa_length": 973,
"cds_start": 693,
"cds_end": null,
"cds_length": 2922,
"cdna_start": 1659,
"cdna_end": null,
"cdna_length": 4218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"hgvs_c": "n.1665A>G",
"hgvs_p": null,
"transcript": "NR_136342.2",
"protein_id": null,
"transcript_support_level": null,
"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": 4129,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ULK4",
"gene_hgnc_id": 15784,
"dbsnp": "rs1716687",
"frequency_reference_population": 0.9846982,
"hom_count_reference_population": 783468,
"allele_count_reference_population": 1586593,
"gnomad_exomes_af": 0.990578,
"gnomad_genomes_af": 0.928369,
"gnomad_exomes_ac": 1445208,
"gnomad_genomes_ac": 141385,
"gnomad_exomes_homalt": 717000,
"gnomad_genomes_homalt": 66468,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"computational_prediction_selected": "Benign",
"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": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.044,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000301831.9",
"gene_symbol": "ULK4",
"hgnc_id": 15784,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1599A>G",
"hgvs_p": "p.Val533Val"
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}