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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: 19-39482885-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=39482885&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 39482885,
"ref": "G",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000607714.6",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.260G>C",
"hgvs_p": "p.Gly87Ala",
"transcript": "NM_001001563.5",
"protein_id": "NP_001001563.2",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 353,
"cds_start": 260,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 276,
"cdna_end": null,
"cdna_length": 5037,
"mane_select": "ENST00000607714.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.260G>C",
"hgvs_p": "p.Gly87Ala",
"transcript": "ENST00000607714.6",
"protein_id": "ENSP00000475531.1",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 353,
"cds_start": 260,
"cds_end": null,
"cds_length": 1062,
"cdna_start": 276,
"cdna_end": null,
"cdna_length": 5037,
"mane_select": "NM_001001563.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.569G>C",
"hgvs_p": "p.Gly190Ala",
"transcript": "ENST00000544017.5",
"protein_id": "ENSP00000445806.2",
"transcript_support_level": 1,
"aa_start": 190,
"aa_end": null,
"aa_length": 456,
"cds_start": 569,
"cds_end": null,
"cds_length": 1371,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 2572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "n.260G>C",
"hgvs_p": null,
"transcript": "ENST00000601358.5",
"protein_id": "ENSP00000472476.2",
"transcript_support_level": 1,
"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": 1481,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.257G>C",
"hgvs_p": "p.Gly86Ala",
"transcript": "ENST00000602028.5",
"protein_id": "ENSP00000470896.1",
"transcript_support_level": 5,
"aa_start": 86,
"aa_end": null,
"aa_length": 255,
"cds_start": 257,
"cds_end": null,
"cds_length": 769,
"cdna_start": 258,
"cdna_end": null,
"cdna_length": 770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.-21G>C",
"hgvs_p": null,
"transcript": "NM_001329559.2",
"protein_id": "NP_001316488.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 240,
"cds_start": -4,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.242G>C",
"hgvs_p": "p.Gly81Ala",
"transcript": "ENST00000594583.2",
"protein_id": "ENSP00000470994.1",
"transcript_support_level": 3,
"aa_start": 81,
"aa_end": null,
"aa_length": 225,
"cds_start": 242,
"cds_end": null,
"cds_length": 678,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 680,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.109G>C",
"hgvs_p": "p.Glu37Gln",
"transcript": "ENST00000597666.5",
"protein_id": "ENSP00000472723.2",
"transcript_support_level": 3,
"aa_start": 37,
"aa_end": null,
"aa_length": 199,
"cds_start": 109,
"cds_end": null,
"cds_length": 600,
"cdna_start": 113,
"cdna_end": null,
"cdna_length": 604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.224G>C",
"hgvs_p": "p.Gly75Ala",
"transcript": "XM_011527491.4",
"protein_id": "XP_011525793.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 341,
"cds_start": 224,
"cds_end": null,
"cds_length": 1026,
"cdna_start": 258,
"cdna_end": null,
"cdna_length": 5019,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.-113G>C",
"hgvs_p": null,
"transcript": "XM_047439681.1",
"protein_id": "XP_047295637.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 229,
"cds_start": -4,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "n.256G>C",
"hgvs_p": null,
"transcript": "ENST00000595286.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 698,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "n.230G>C",
"hgvs_p": null,
"transcript": "ENST00000597782.5",
"protein_id": "ENSP00000469052.1",
"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": 456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "n.268G>C",
"hgvs_p": null,
"transcript": "ENST00000598125.5",
"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": 577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "n.185G>C",
"hgvs_p": null,
"transcript": "ENST00000599733.5",
"protein_id": "ENSP00000472904.1",
"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": 669,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "n.185G>C",
"hgvs_p": null,
"transcript": "ENST00000602265.5",
"protein_id": "ENSP00000472920.1",
"transcript_support_level": 2,
"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": 786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.-21G>C",
"hgvs_p": null,
"transcript": "NM_001329559.2",
"protein_id": "NP_001316488.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 240,
"cds_start": -4,
"cds_end": null,
"cds_length": 723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.-113G>C",
"hgvs_p": null,
"transcript": "XM_047439681.1",
"protein_id": "XP_047295637.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 229,
"cds_start": -4,
"cds_end": null,
"cds_length": 690,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5000,
"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": 7,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.259+852G>C",
"hgvs_p": null,
"transcript": "ENST00000601403.5",
"protein_id": "ENSP00000472184.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 255,
"cds_start": -4,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 769,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"hgvs_c": "c.108+1924G>C",
"hgvs_p": null,
"transcript": "ENST00000599794.5",
"protein_id": "ENSP00000472524.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 157,
"cds_start": -4,
"cds_end": null,
"cds_length": 474,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TIMM50",
"gene_hgnc_id": 23656,
"dbsnp": "rs776019250",
"frequency_reference_population": 6.840591e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84059e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7140080332756042,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.9520000219345093,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.415,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.81,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.925,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.04,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999241879645801,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000607714.6",
"gene_symbol": "TIMM50",
"hgnc_id": 23656,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.260G>C",
"hgvs_p": "p.Gly87Ala"
}
],
"clinvar_disease": "3-methylglutaconic aciduria type 9,Mitochondrial encephalopathy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Mitochondrial encephalopathy|3-methylglutaconic aciduria type 9",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}