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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: 5-61098995-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=61098995&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 61098995,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000296597.10",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "c.221G>A",
"hgvs_p": "p.Trp74*",
"transcript": "NM_174889.5",
"protein_id": "NP_777549.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 169,
"cds_start": 221,
"cds_end": null,
"cds_length": 510,
"cdna_start": 272,
"cdna_end": null,
"cdna_length": 632,
"mane_select": "ENST00000296597.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "c.221G>A",
"hgvs_p": "p.Trp74*",
"transcript": "ENST00000296597.10",
"protein_id": "ENSP00000296597.5",
"transcript_support_level": 1,
"aa_start": 74,
"aa_end": null,
"aa_length": 169,
"cds_start": 221,
"cds_end": null,
"cds_length": 510,
"cdna_start": 272,
"cdna_end": null,
"cdna_length": 632,
"mane_select": "NM_174889.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "c.177G>A",
"hgvs_p": "p.Leu59Leu",
"transcript": "ENST00000511107.1",
"protein_id": "ENSP00000423377.1",
"transcript_support_level": 1,
"aa_start": 59,
"aa_end": null,
"aa_length": 60,
"cds_start": 177,
"cds_end": null,
"cds_length": 183,
"cdna_start": 226,
"cdna_end": null,
"cdna_length": 586,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "c.136+25781G>A",
"hgvs_p": null,
"transcript": "ENST00000502658.1",
"protein_id": "ENSP00000426149.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 50,
"cds_start": -4,
"cds_end": null,
"cds_length": 153,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 461,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "c.221G>A",
"hgvs_p": "p.Trp74*",
"transcript": "ENST00000677932.1",
"protein_id": "ENSP00000504750.1",
"transcript_support_level": null,
"aa_start": 74,
"aa_end": null,
"aa_length": 177,
"cds_start": 221,
"cds_end": null,
"cds_length": 534,
"cdna_start": 254,
"cdna_end": null,
"cdna_length": 4520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "n.346G>A",
"hgvs_p": null,
"transcript": "ENST00000512623.1",
"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": 696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "n.*237G>A",
"hgvs_p": null,
"transcript": "ENST00000677756.1",
"protein_id": "ENSP00000503642.1",
"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": 843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "n.*51G>A",
"hgvs_p": null,
"transcript": "ENST00000678452.1",
"protein_id": "ENSP00000504248.1",
"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": 2211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "n.*237G>A",
"hgvs_p": null,
"transcript": "ENST00000677756.1",
"protein_id": "ENSP00000503642.1",
"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": 843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"hgvs_c": "n.*51G>A",
"hgvs_p": null,
"transcript": "ENST00000678452.1",
"protein_id": "ENSP00000504248.1",
"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": 2211,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NDUFAF2",
"gene_hgnc_id": 28086,
"dbsnp": "rs772294726",
"frequency_reference_population": 0.000022528837,
"hom_count_reference_population": 0,
"allele_count_reference_population": 36,
"gnomad_exomes_af": 0.0000235126,
"gnomad_genomes_af": 0.000013165,
"gnomad_exomes_ac": 34,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5899999737739563,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.3499999940395355,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.59,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.557,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.35,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000296597.10",
"gene_symbol": "NDUFAF2",
"hgnc_id": 28086,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.221G>A",
"hgvs_p": "p.Trp74*"
}
],
"clinvar_disease": " nuclear type 10,Leigh syndrome,Mitochondrial complex I deficiency,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:3",
"phenotype_combined": "Leigh syndrome|not provided|Mitochondrial complex I deficiency, nuclear type 10",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}