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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: 15-89318535-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=89318535&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 89318535,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000268124.11",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.3482+6C>T",
"hgvs_p": null,
"transcript": "NM_002693.3",
"protein_id": "NP_002684.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1239,
"cds_start": -4,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4462,
"mane_select": "ENST00000268124.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.3482+6C>T",
"hgvs_p": null,
"transcript": "ENST00000268124.11",
"protein_id": "ENSP00000268124.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1239,
"cds_start": -4,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4462,
"mane_select": "NM_002693.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.3482+6C>T",
"hgvs_p": null,
"transcript": "ENST00000442287.6",
"protein_id": "ENSP00000399851.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1239,
"cds_start": -4,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4487,
"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": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.3686C>T",
"hgvs_p": null,
"transcript": "ENST00000672071.1",
"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": 5318,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.665C>T",
"hgvs_p": null,
"transcript": "ENST00000672695.1",
"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": 1930,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.3482+6C>T",
"hgvs_p": null,
"transcript": "NM_001126131.2",
"protein_id": "NP_001119603.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1239,
"cds_start": -4,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.3482+6C>T",
"hgvs_p": null,
"transcript": "ENST00000636937.2",
"protein_id": "ENSP00000516154.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1239,
"cds_start": -4,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 18,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.2552+6C>T",
"hgvs_p": null,
"transcript": "ENST00000637264.1",
"protein_id": "ENSP00000489844.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 909,
"cds_start": -4,
"cds_end": null,
"cds_length": 2730,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3153,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.3083+6C>T",
"hgvs_p": null,
"transcript": "ENST00000530292.3",
"protein_id": "ENSP00000432885.2",
"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": 3843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.*2906+6C>T",
"hgvs_p": null,
"transcript": "ENST00000631044.2",
"protein_id": "ENSP00000486730.1",
"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": 4668,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.*552+6C>T",
"hgvs_p": null,
"transcript": "ENST00000635986.2",
"protein_id": "ENSP00000490653.2",
"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": 4388,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.*2049+6C>T",
"hgvs_p": null,
"transcript": "ENST00000636774.1",
"protein_id": "ENSP00000489799.1",
"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": 4151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.*1589+6C>T",
"hgvs_p": null,
"transcript": "ENST00000637238.1",
"protein_id": "ENSP00000490756.1",
"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": 3022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.*2124+6C>T",
"hgvs_p": null,
"transcript": "ENST00000666746.1",
"protein_id": "ENSP00000499495.1",
"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": 3698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.3482+6C>T",
"hgvs_p": null,
"transcript": "ENST00000672923.2",
"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": 4130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"dbsnp": "rs55779802",
"frequency_reference_population": 0.00016006373,
"hom_count_reference_population": 3,
"allele_count_reference_population": 258,
"gnomad_exomes_af": 0.000118534,
"gnomad_genomes_af": 0.000557904,
"gnomad_exomes_ac": 173,
"gnomad_genomes_ac": 85,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7300000190734863,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.685,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000116855814842379,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000268124.11",
"gene_symbol": "POLG",
"hgnc_id": 9179,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3482+6C>T",
"hgvs_p": null
}
],
"clinvar_disease": " and ophthalmoparesis, autosomal dominant 1, autosomal recessive 1, dysarthria,Hereditary spastic paraplegia,Mitochondrial DNA depletion syndrome 4b,POLG-Related Spectrum Disorders,Progressive external ophthalmoplegia with mitochondrial DNA deletions,Progressive sclerosing poliodystrophy,Sensory ataxic neuropathy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:5 LB:3 B:1",
"phenotype_combined": "not specified|POLG-Related Spectrum Disorders|Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1;Mitochondrial DNA depletion syndrome 4b;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1;Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis;Progressive sclerosing poliodystrophy|Progressive sclerosing poliodystrophy|not provided|Hereditary spastic paraplegia|Mitochondrial DNA depletion syndrome 4b",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}