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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: 7-102638754-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=102638754&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 102638754,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001114403.3",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPK3BL1",
"gene_hgnc_id": 37278,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "NM_001114403.3",
"protein_id": "NP_001107875.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 263,
"cds_start": 643,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000340457.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001114403.3"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPK3BL1",
"gene_hgnc_id": 37278,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "ENST00000340457.8",
"protein_id": "ENSP00000342938.8",
"transcript_support_level": 1,
"aa_start": 215,
"aa_end": null,
"aa_length": 263,
"cds_start": 643,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001114403.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000340457.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLR2J2-UPK3BL1",
"gene_hgnc_id": 58364,
"hgvs_c": "n.*585G>A",
"hgvs_p": null,
"transcript": "ENST00000476151.5",
"protein_id": "ENSP00000418603.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000476151.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000205236",
"gene_hgnc_id": null,
"hgvs_c": "n.643G>A",
"hgvs_p": null,
"transcript": "ENST00000519541.1",
"protein_id": "ENSP00000429397.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000519541.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLR2J2-UPK3BL1",
"gene_hgnc_id": 58364,
"hgvs_c": "n.*585G>A",
"hgvs_p": null,
"transcript": "ENST00000476151.5",
"protein_id": "ENSP00000418603.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000476151.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPK3BL1",
"gene_hgnc_id": 37278,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "ENST00000962212.1",
"protein_id": "ENSP00000632271.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 275,
"cds_start": 643,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000962212.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPK3BL1",
"gene_hgnc_id": 37278,
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile",
"transcript": "ENST00000868524.1",
"protein_id": "ENSP00000538583.1",
"transcript_support_level": null,
"aa_start": 215,
"aa_end": null,
"aa_length": 260,
"cds_start": 643,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000868524.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLR2J2-UPK3BL1",
"gene_hgnc_id": null,
"hgvs_c": "n.995G>A",
"hgvs_p": null,
"transcript": "NR_173352.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_173352.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000279168",
"gene_hgnc_id": null,
"hgvs_c": "n.949+39593G>A",
"hgvs_p": null,
"transcript": "ENST00000639209.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000639209.1"
}
],
"gene_symbol": "UPK3BL1",
"gene_hgnc_id": 37278,
"dbsnp": "rs1234025624",
"frequency_reference_population": null,
"hom_count_reference_population": null,
"allele_count_reference_population": null,
"gnomad_exomes_af": 0.0000189571,
"gnomad_genomes_af": 0.0000337,
"gnomad_exomes_ac": 19,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09140411019325256,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.028,
"revel_prediction": "Benign",
"alphamissense_score": 0.084,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.6,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.348,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001114403.3",
"gene_symbol": "UPK3BL1",
"hgnc_id": 37278,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.643G>A",
"hgvs_p": "p.Val215Ile"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000476151.5",
"gene_symbol": "POLR2J2-UPK3BL1",
"hgnc_id": 58364,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*585G>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000519541.1",
"gene_symbol": "ENSG00000205236",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.643G>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000639209.1",
"gene_symbol": "ENSG00000279168",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.949+39593G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}