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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: 17-64477864-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=64477864&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 64477864,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000539111.7",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "c.1417G>A",
"hgvs_p": "p.Asp473Asn",
"transcript": "NM_007215.4",
"protein_id": "NP_009146.2",
"transcript_support_level": null,
"aa_start": 473,
"aa_end": null,
"aa_length": 485,
"cds_start": 1417,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1503,
"cdna_end": null,
"cdna_length": 1582,
"mane_select": "ENST00000539111.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "c.1417G>A",
"hgvs_p": "p.Asp473Asn",
"transcript": "ENST00000539111.7",
"protein_id": "ENSP00000442563.2",
"transcript_support_level": 1,
"aa_start": 473,
"aa_end": null,
"aa_length": 485,
"cds_start": 1417,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1503,
"cdna_end": null,
"cdna_length": 1582,
"mane_select": "NM_007215.4",
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "n.1589G>A",
"hgvs_p": null,
"transcript": "ENST00000585104.2",
"protein_id": null,
"transcript_support_level": 3,
"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": 1601,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "n.*319G>A",
"hgvs_p": null,
"transcript": "ENST00000671755.1",
"protein_id": "ENSP00000500690.1",
"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": 1557,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "n.*2508G>A",
"hgvs_p": null,
"transcript": "ENST00000673460.1",
"protein_id": "ENSP00000500198.1",
"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": 3559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "c.*119G>A",
"hgvs_p": null,
"transcript": "ENST00000581355.1",
"protein_id": "ENSP00000462071.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": -4,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 652,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "n.*319G>A",
"hgvs_p": null,
"transcript": "ENST00000671755.1",
"protein_id": "ENSP00000500690.1",
"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": 1557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "n.*2508G>A",
"hgvs_p": null,
"transcript": "ENST00000673460.1",
"protein_id": "ENSP00000500198.1",
"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": 3559,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "c.*60G>A",
"hgvs_p": null,
"transcript": "XM_047435222.1",
"protein_id": "XP_047291178.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 408,
"cds_start": -4,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1452,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "c.*119G>A",
"hgvs_p": null,
"transcript": "XM_047435223.1",
"protein_id": "XP_047291179.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 398,
"cds_start": -4,
"cds_end": null,
"cds_length": 1197,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MILR1",
"gene_hgnc_id": 27570,
"hgvs_c": "c.*28+10219C>T",
"hgvs_p": null,
"transcript": "ENST00000718368.1",
"protein_id": "ENSP00000520798.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 343,
"cds_start": -4,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MILR1",
"gene_hgnc_id": 27570,
"hgvs_c": "c.*28+10219C>T",
"hgvs_p": null,
"transcript": "XM_024450708.2",
"protein_id": "XP_024306476.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 343,
"cds_start": -4,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MILR1",
"gene_hgnc_id": 27570,
"hgvs_c": "c.*28+10219C>T",
"hgvs_p": null,
"transcript": "XM_047435791.1",
"protein_id": "XP_047291747.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 343,
"cds_start": -4,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MILR1",
"gene_hgnc_id": 27570,
"hgvs_c": "n.1114+10219C>T",
"hgvs_p": null,
"transcript": "XR_002957989.2",
"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": 1375,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "MILR1",
"gene_hgnc_id": 27570,
"hgvs_c": "n.1114+10219C>T",
"hgvs_p": null,
"transcript": "XR_002957990.2",
"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": 2213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"hgvs_c": "n.*100G>A",
"hgvs_p": null,
"transcript": "ENST00000582501.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "POLG2",
"gene_hgnc_id": 9180,
"dbsnp": "rs563130304",
"frequency_reference_population": 0.00011985925,
"hom_count_reference_population": 2,
"allele_count_reference_population": 193,
"gnomad_exomes_af": 0.000122086,
"gnomad_genomes_af": 0.0000985338,
"gnomad_exomes_ac": 178,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01868841052055359,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.411,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1115,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.514,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000539111.7",
"gene_symbol": "POLG2",
"hgnc_id": 9180,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.1417G>A",
"hgvs_p": "p.Asp473Asn"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000718368.1",
"gene_symbol": "MILR1",
"hgnc_id": 27570,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*28+10219C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal dominant 4,Hereditary spastic paraplegia,Progressive external ophthalmoplegia with mitochondrial DNA deletions,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:3",
"phenotype_combined": "not provided|Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4|Hereditary spastic paraplegia",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}