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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: 15-89333596-TTGCTGCTGCTGC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=89333596&ref=TTGCTGCTGCTGC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 89333596,
"ref": "TTGCTGCTGCTGC",
"alt": "T",
"effect": "conservative_inframe_deletion",
"transcript": "NM_001430120.1",
"consequences": [
{
"aa_ref": "AAAA",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLGARF",
"gene_hgnc_id": 56246,
"hgvs_c": "c.202_213delGCAGCAGCAGCA",
"hgvs_p": "p.Ala68_Ala71del",
"transcript": "NM_001430120.1",
"protein_id": "NP_001417049.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 260,
"cds_start": 202,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000706918.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001430120.1"
},
{
"aa_ref": "AAAA",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLGARF",
"gene_hgnc_id": 56246,
"hgvs_c": "c.202_213delGCAGCAGCAGCA",
"hgvs_p": "p.Ala68_Ala71del",
"transcript": "ENST00000706918.1",
"protein_id": "ENSP00000516626.1",
"transcript_support_level": null,
"aa_start": 68,
"aa_end": null,
"aa_length": 260,
"cds_start": 202,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001430120.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000706918.1"
},
{
"aa_ref": "QQQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.147_158delGCAGCAGCAGCA",
"hgvs_p": "p.Gln50_Gln53del",
"transcript": "NM_002693.3",
"protein_id": "NP_002684.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 1239,
"cds_start": 147,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000268124.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002693.3"
},
{
"aa_ref": "QQQQQ",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.147_158delGCAGCAGCAGCA",
"hgvs_p": "p.Gln50_Gln53del",
"transcript": "ENST00000268124.11",
"protein_id": "ENSP00000268124.5",
"transcript_support_level": 1,
"aa_start": 49,
"aa_end": null,
"aa_length": 1239,
"cds_start": 147,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002693.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000268124.11"
},
{
"aa_ref": "QQQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.147_158delGCAGCAGCAGCA",
"hgvs_p": "p.Gln50_Gln53del",
"transcript": "ENST00000442287.6",
"protein_id": "ENSP00000399851.2",
"transcript_support_level": 1,
"aa_start": 49,
"aa_end": null,
"aa_length": 1239,
"cds_start": 147,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442287.6"
},
{
"aa_ref": "QQQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.147_158delGCAGCAGCAGCA",
"hgvs_p": "p.Gln50_Gln53del",
"transcript": "NM_001126131.2",
"protein_id": "NP_001119603.1",
"transcript_support_level": null,
"aa_start": 49,
"aa_end": null,
"aa_length": 1239,
"cds_start": 147,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001126131.2"
},
{
"aa_ref": "QQQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "c.147_158delGCAGCAGCAGCA",
"hgvs_p": "p.Gln50_Gln53del",
"transcript": "ENST00000636937.2",
"protein_id": "ENSP00000516154.1",
"transcript_support_level": 5,
"aa_start": 49,
"aa_end": null,
"aa_length": 1239,
"cds_start": 147,
"cds_end": null,
"cds_length": 3720,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000636937.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.147_158delGCAGCAGCAGCA",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000631044.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.147_158delGCAGCAGCAGCA",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000635986.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.147_158delGCAGCAGCAGCA",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000636774.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.345_356delGCAGCAGCAGCA",
"hgvs_p": null,
"transcript": "ENST00000672071.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000672071.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.-253_-242delGCAGCAGCAGCA",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000530292.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.-199_-188delGCAGCAGCAGCA",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000666746.1"
},
{
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "POLG",
"gene_hgnc_id": 9179,
"hgvs_c": "n.*242_*253delGCAGCAGCAGCA",
"hgvs_p": null,
"transcript": "ENST00000637711.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000637711.1"
}
],
"gene_symbol": "POLGARF",
"gene_hgnc_id": 56246,
"dbsnp": "rs41550117",
"frequency_reference_population": 0.0006926967,
"hom_count_reference_population": 4,
"allele_count_reference_population": 1107,
"gnomad_exomes_af": 0.000646435,
"gnomad_genomes_af": 0.00113376,
"gnomad_exomes_ac": 935,
"gnomad_genomes_ac": 172,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.075,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,BP3,BP6,BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP3",
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001430120.1",
"gene_symbol": "POLGARF",
"hgnc_id": 56246,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "",
"hgvs_c": "c.202_213delGCAGCAGCAGCA",
"hgvs_p": "p.Ala68_Ala71del"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP6",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_002693.3",
"gene_symbol": "POLG",
"hgnc_id": 9179,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.147_158delGCAGCAGCAGCA",
"hgvs_p": "p.Gln50_Gln53del"
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Inborn genetic diseases,Progressive sclerosing poliodystrophy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:6 B:2",
"phenotype_combined": "not specified|Progressive sclerosing poliodystrophy|not provided|Hereditary spastic paraplegia|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}