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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: 15-89327201-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=89327201&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PS3",
"PM5",
"PP5"
],
"effects": [
"missense_variant"
],
"gene_symbol": "POLG",
"hgnc_id": 9179,
"hgvs_c": "c.1399G>A",
"hgvs_p": "p.Ala467Thr",
"inheritance_mode": "AR,AD",
"pathogenic_score": 7,
"score": 7,
"transcript": "NM_002693.3",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PS3,PM5,PP5",
"acmg_score": 7,
"allele_count_reference_population": 1637,
"alphamissense_prediction": null,
"alphamissense_score": 0.7688,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.41,
"chr": "15",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": " and ophthalmoparesis, autosomal dominant 1, autosomal recessive 1, dysarthria,Hereditary spastic paraplegia,Inborn genetic diseases,Intellectual disability,Mitochondrial DNA depletion syndrome 4b,Mitochondrial disease,Neurodevelopmental delay,POLG-Related Spectrum Disorders,POLG-related disorder,Progressive external ophthalmoplegia with mitochondrial DNA deletions,Progressive sclerosing poliodystrophy,Sensory ataxic neuropathy,Spinocerebellar ataxia with epilepsy,Tip-toe gait,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:41 LB:1 O:2",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.726177453994751,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "T",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "A",
"aa_start": 467,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4462,
"cdna_start": 1710,
"cds_end": null,
"cds_length": 3720,
"cds_start": 1399,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_002693.3",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.1399G>A",
"hgvs_p": "p.Ala467Thr",
"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": "T",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "A",
"aa_start": 467,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4462,
"cdna_start": 1710,
"cds_end": null,
"cds_length": 3720,
"cds_start": 1399,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000268124.11",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.1399G>A",
"hgvs_p": "p.Ala467Thr",
"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": "T",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "A",
"aa_start": 467,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4487,
"cdna_start": 1735,
"cds_end": null,
"cds_length": 3720,
"cds_start": 1399,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000442287.6",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.1399G>A",
"hgvs_p": "p.Ala467Thr",
"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": "T",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "A",
"aa_start": 467,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4450,
"cdna_start": 1698,
"cds_end": null,
"cds_length": 3720,
"cds_start": 1399,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001126131.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.1399G>A",
"hgvs_p": "p.Ala467Thr",
"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": "T",
"aa_end": null,
"aa_length": 1239,
"aa_ref": "A",
"aa_start": 467,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5095,
"cdna_start": 2343,
"cds_end": null,
"cds_length": 3720,
"cds_start": 1399,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000636937.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.1399G>A",
"hgvs_p": "p.Ala467Thr",
"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": "T",
"aa_end": null,
"aa_length": 909,
"aa_ref": "A",
"aa_start": 157,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3153,
"cdna_start": 471,
"cds_end": null,
"cds_length": 2730,
"cds_start": 469,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000637264.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "c.469G>A",
"hgvs_p": "p.Ala157Thr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489844.1",
"strand": false,
"transcript": "ENST00000637264.1",
"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": 3843,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 23,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000530292.3",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.1000G>A",
"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": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 445,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000532363.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.257G>A",
"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": "ENST00000532363.2",
"transcript_support_level": 2
},
{
"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": 8,
"exon_rank_end": null,
"feature": "ENST00000631044.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.*782G>A",
"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": 7,
"exon_rank_end": null,
"feature": "ENST00000635986.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.1399G>A",
"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": 7,
"exon_rank_end": null,
"feature": "ENST00000636774.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.1399G>A",
"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": 3022,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000637238.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.136G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000490756.1",
"strand": false,
"transcript": "ENST00000637238.1",
"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": 5,
"exon_rank_end": null,
"feature": "ENST00000666746.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.*41G>A",
"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": 7,
"exon_rank_end": null,
"feature": "ENST00000672071.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.1597G>A",
"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": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 4130,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 18,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000672923.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.1502G>A",
"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": "ENST00000672923.2",
"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": 8,
"exon_rank_end": null,
"feature": "ENST00000631044.2",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.*782G>A",
"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": 3698,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 21,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000666746.1",
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"hgvs_c": "n.*41G>A",
"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
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs113994095",
"effect": "missense_variant",
"frequency_reference_population": 0.0010140894,
"gene_hgnc_id": 9179,
"gene_symbol": "POLG",
"gnomad_exomes_ac": 1537,
"gnomad_exomes_af": 0.00105138,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 100,
"gnomad_genomes_af": 0.000656289,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1|Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis|Spinocerebellar ataxia with epilepsy|Progressive sclerosing poliodystrophy|Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1|POLG-Related Spectrum Disorders|not provided|Mitochondrial disease|Neurodevelopmental delay|Mitochondrial DNA depletion syndrome 4b;Progressive sclerosing poliodystrophy|POLG-related disorder|Mitochondrial DNA depletion syndrome 4b;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;Progressive sclerosing poliodystrophy|Hereditary spastic paraplegia|Mitochondrial DNA depletion syndrome 4b|Tip-toe gait|Mitochondrial DNA depletion syndrome 4b;Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1;Sensory ataxic neuropathy, dysarthria, and ophthalmoparesis;Progressive sclerosing poliodystrophy|Intellectual disability|Inborn genetic diseases",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 7.468,
"pos": 89327201,
"ref": "C",
"revel_prediction": "Pathogenic",
"revel_score": 0.884,
"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"
}
]
}