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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: 15-89330133-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=89330133&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"PP3",
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "POLG",
"hgnc_id": 9179,
"hgvs_c": "c.803G>C",
"hgvs_p": "p.Gly268Ala",
"inheritance_mode": "AR,AD",
"pathogenic_score": 1,
"score": -8,
"transcript": "NM_002693.3",
"verdict": "Benign"
},
{
"benign_score": 9,
"criteria": [
"PP3",
"BP4_Strong",
"BP6",
"BS2"
],
"effects": [
"downstream_gene_variant"
],
"gene_symbol": "POLGARF",
"hgnc_id": 56246,
"hgvs_c": "c.*75G>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 1,
"score": -8,
"transcript": "NM_001430120.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP4_Strong,BP6,BS2",
"acmg_score": -8,
"allele_count_reference_population": 6380,
"alphamissense_prediction": null,
"alphamissense_score": 0.8408,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.5,
"chr": "15",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " and ophthalmoparesis, autosomal dominant 1, autosomal recessive 1, dysarthria,Charcot-Marie-Tooth disease axonal type 2U,Hereditary spastic paraplegia,Inborn genetic diseases,Mitochondrial DNA depletion syndrome 4b,POLG-Related Spectrum Disorders,POLG-related disorder,Progressive external ophthalmoplegia with mitochondrial DNA deletions,Progressive sclerosing poliodystrophy,Sensory ataxic neuropathy,Tip-toe gait,not provided,not specified",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:9 LB:7 B:2 O:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.053885579109191895,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "G",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4462,
"cdna_start": 1114,
"cds_end": null,
"cds_length": 3720,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_002693.3",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.803G>C",
"hgvs_p": "p.Gly268Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000268124.11",
"protein_coding": true,
"protein_id": "NP_002684.1",
"strand": false,
"transcript": "NM_002693.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "G",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4462,
"cdna_start": 1114,
"cds_end": null,
"cds_length": 3720,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000268124.11",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.803G>C",
"hgvs_p": "p.Gly268Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002693.3",
"protein_coding": true,
"protein_id": "ENSP00000268124.5",
"strand": false,
"transcript": "ENST00000268124.11",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "G",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4487,
"cdna_start": 1139,
"cds_end": null,
"cds_length": 3720,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000442287.6",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.803G>C",
"hgvs_p": "p.Gly268Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000399851.2",
"strand": false,
"transcript": "ENST00000442287.6",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "G",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4450,
"cdna_start": 1102,
"cds_end": null,
"cds_length": 3720,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001126131.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.803G>C",
"hgvs_p": "p.Gly268Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001119603.1",
"strand": false,
"transcript": "NM_001126131.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "G",
"aa_start": 268,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5095,
"cdna_start": 1747,
"cds_end": null,
"cds_length": 3720,
"cds_start": 803,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000636937.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.803G>C",
"hgvs_p": "p.Gly268Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516154.1",
"strand": false,
"transcript": "ENST00000636937.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3843,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000530292.3",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.404G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000432885.2",
"strand": false,
"transcript": "ENST00000530292.3",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4668,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000631044.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.*186G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000486730.1",
"strand": false,
"transcript": "ENST00000631044.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4388,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000635986.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.803G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490653.2",
"strand": false,
"transcript": "ENST00000635986.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4151,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000636774.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.803G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000489799.1",
"strand": false,
"transcript": "ENST00000636774.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3698,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000666746.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.458G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000499495.1",
"strand": false,
"transcript": "ENST00000666746.1",
"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": 5318,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 22,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000672071.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.1001G>C",
"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": "ENST00000672071.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 4668,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 24,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000631044.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.*186G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000486730.1",
"strand": false,
"transcript": "ENST00000631044.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 260,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 783,
"cdna_start": null,
"cds_end": null,
"cds_length": 783,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001430120.1",
"gene_hgnc_id": 56246,
"gene_symbol": "POLGARF",
"hgvs_c": "c.*75G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000706918.1",
"protein_coding": true,
"protein_id": "NP_001417049.1",
"strand": true,
"transcript": "NM_001430120.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 260,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 783,
"cdna_start": null,
"cds_end": null,
"cds_length": 783,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000706918.1",
"gene_hgnc_id": 56246,
"gene_symbol": "POLGARF",
"hgvs_c": "c.*75G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001430120.1",
"protein_coding": true,
"protein_id": "ENSP00000516626.1",
"strand": true,
"transcript": "ENST00000706918.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 31,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 100,
"cdna_start": null,
"cds_end": null,
"cds_length": 98,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000637307.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.*78G>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000490427.1",
"strand": true,
"transcript": "ENST00000637307.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs61752784",
"effect": "missense_variant",
"frequency_reference_population": 0.0039527602,
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"gnomad_exomes_ac": 5843,
"gnomad_exomes_af": 0.00399735,
"gnomad_exomes_homalt": 17,
"gnomad_genomes_ac": 537,
"gnomad_genomes_af": 0.00352496,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 18,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "not specified|Progressive sclerosing poliodystrophy|POLG-related disorder|not provided|Inborn genetic diseases|Hereditary spastic paraplegia|Tip-toe gait|Progressive sclerosing poliodystrophy;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1;Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis;Mitochondrial DNA depletion syndrome 4b|POLG-Related Spectrum Disorders|Charcot-Marie-Tooth disease axonal type 2U",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.87,
"pos": 89330133,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.967,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_002693.3"
}
]
}