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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: 7-101206426-CA-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=101206426&ref=CA&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 101206426,
"ref": "CA",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "NM_001084.5",
"consequences": [
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2071delT",
"hgvs_p": "p.Cys691fs",
"transcript": "NM_001084.5",
"protein_id": "NP_001075.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 738,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000223127.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001084.5"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2071delT",
"hgvs_p": "p.Cys691fs",
"transcript": "ENST00000223127.8",
"protein_id": "ENSP00000223127.3",
"transcript_support_level": 1,
"aa_start": 691,
"aa_end": null,
"aa_length": 738,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001084.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000223127.8"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2143delT",
"hgvs_p": "p.Cys715fs",
"transcript": "ENST00000890272.1",
"protein_id": "ENSP00000560331.1",
"transcript_support_level": null,
"aa_start": 715,
"aa_end": null,
"aa_length": 762,
"cds_start": 2143,
"cds_end": null,
"cds_length": 2289,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890272.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2071delT",
"hgvs_p": "p.Cys691fs",
"transcript": "ENST00000890269.1",
"protein_id": "ENSP00000560328.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 738,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890269.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2071delT",
"hgvs_p": "p.Cys691fs",
"transcript": "ENST00000890270.1",
"protein_id": "ENSP00000560329.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 738,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890270.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2071delT",
"hgvs_p": "p.Cys691fs",
"transcript": "ENST00000890271.1",
"protein_id": "ENSP00000560330.1",
"transcript_support_level": null,
"aa_start": 691,
"aa_end": null,
"aa_length": 738,
"cds_start": 2071,
"cds_end": null,
"cds_length": 2217,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890271.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2044delT",
"hgvs_p": "p.Cys682fs",
"transcript": "ENST00000890275.1",
"protein_id": "ENSP00000560334.1",
"transcript_support_level": null,
"aa_start": 682,
"aa_end": null,
"aa_length": 729,
"cds_start": 2044,
"cds_end": null,
"cds_length": 2190,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890275.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2014delT",
"hgvs_p": "p.Cys672fs",
"transcript": "ENST00000890276.1",
"protein_id": "ENSP00000560335.1",
"transcript_support_level": null,
"aa_start": 672,
"aa_end": null,
"aa_length": 719,
"cds_start": 2014,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890276.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.2011delT",
"hgvs_p": "p.Cys671fs",
"transcript": "ENST00000890274.1",
"protein_id": "ENSP00000560333.1",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 718,
"cds_start": 2011,
"cds_end": null,
"cds_length": 2157,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890274.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.1909delT",
"hgvs_p": "p.Cys637fs",
"transcript": "ENST00000890273.1",
"protein_id": "ENSP00000560332.1",
"transcript_support_level": null,
"aa_start": 637,
"aa_end": null,
"aa_length": 684,
"cds_start": 1909,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890273.1"
},
{
"aa_ref": "C",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"hgvs_c": "c.646delT",
"hgvs_p": "p.Cys216fs",
"transcript": "ENST00000454310.5",
"protein_id": "ENSP00000407555.1",
"transcript_support_level": 5,
"aa_start": 216,
"aa_end": null,
"aa_length": 263,
"cds_start": 646,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000454310.5"
}
],
"gene_symbol": "PLOD3",
"gene_hgnc_id": 9083,
"dbsnp": "rs786205872",
"frequency_reference_population": 6.878904e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.8789e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"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,
"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": 9.22,
"phylop100way_prediction": "Pathogenic",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Moderate,PM2,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001084.5",
"gene_symbol": "PLOD3",
"hgnc_id": 9083,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2071delT",
"hgvs_p": "p.Cys691fs"
}
],
"clinvar_disease": " and deafness, arterial rupture,Bone fragility with contractures",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Bone fragility with contractures, arterial rupture, and deafness",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}