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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: 19-17341078-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=17341078&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 17341078,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_133644.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Asp337His",
"transcript": "NM_032620.4",
"protein_id": "NP_116009.2",
"transcript_support_level": null,
"aa_start": 337,
"aa_end": null,
"aa_length": 492,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000324894.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032620.4"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.1009G>C",
"hgvs_p": "p.Asp337His",
"transcript": "ENST00000324894.13",
"protein_id": "ENSP00000313818.7",
"transcript_support_level": 1,
"aa_start": 337,
"aa_end": null,
"aa_length": 492,
"cds_start": 1009,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032620.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000324894.13"
},
{
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.975-29G>C",
"hgvs_p": null,
"transcript": "ENST00000600625.5",
"protein_id": "ENSP00000473150.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 471,
"cds_start": null,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000600625.5"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.1105G>C",
"hgvs_p": "p.Asp369His",
"transcript": "NM_133644.4",
"protein_id": "NP_598399.2",
"transcript_support_level": null,
"aa_start": 369,
"aa_end": null,
"aa_length": 524,
"cds_start": 1105,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_133644.4"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.1105G>C",
"hgvs_p": "p.Asp369His",
"transcript": "ENST00000358792.11",
"protein_id": "ENSP00000351644.6",
"transcript_support_level": 2,
"aa_start": 369,
"aa_end": null,
"aa_length": 524,
"cds_start": 1105,
"cds_end": null,
"cds_length": 1575,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358792.11"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.1075G>C",
"hgvs_p": "p.Asp359His",
"transcript": "NM_001195422.1",
"protein_id": "NP_001182351.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 514,
"cds_start": 1075,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001195422.1"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.1075G>C",
"hgvs_p": "p.Asp359His",
"transcript": "ENST00000361619.9",
"protein_id": "ENSP00000354598.4",
"transcript_support_level": 2,
"aa_start": 359,
"aa_end": null,
"aa_length": 514,
"cds_start": 1075,
"cds_end": null,
"cds_length": 1545,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361619.9"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.952G>C",
"hgvs_p": "p.Asp318His",
"transcript": "ENST00000934088.1",
"protein_id": "ENSP00000604147.1",
"transcript_support_level": null,
"aa_start": 318,
"aa_end": null,
"aa_length": 473,
"cds_start": 952,
"cds_end": null,
"cds_length": 1422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934088.1"
},
{
"aa_ref": "D",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.865G>C",
"hgvs_p": "p.Asp289His",
"transcript": "ENST00000934087.1",
"protein_id": "ENSP00000604146.1",
"transcript_support_level": null,
"aa_start": 289,
"aa_end": null,
"aa_length": 444,
"cds_start": 865,
"cds_end": null,
"cds_length": 1335,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934087.1"
},
{
"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": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "c.975-29G>C",
"hgvs_p": null,
"transcript": "NM_001128855.3",
"protein_id": "NP_001122327.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 471,
"cds_start": null,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001128855.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.133G>C",
"hgvs_p": null,
"transcript": "ENST00000595194.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000595194.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.246G>C",
"hgvs_p": null,
"transcript": "ENST00000596125.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000596125.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.*252G>C",
"hgvs_p": null,
"transcript": "ENST00000598493.5",
"protein_id": "ENSP00000472156.1",
"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": "ENST00000598493.5"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.614G>C",
"hgvs_p": null,
"transcript": "ENST00000602056.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000602056.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.*252G>C",
"hgvs_p": null,
"transcript": "ENST00000598493.5",
"protein_id": "ENSP00000472156.1",
"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": "ENST00000598493.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.1871-29G>C",
"hgvs_p": null,
"transcript": "ENST00000598038.5",
"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": "ENST00000598038.5"
},
{
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"hgvs_c": "n.*252G>C",
"hgvs_p": null,
"transcript": "ENST00000594018.5",
"protein_id": "ENSP00000471421.1",
"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": "ENST00000594018.5"
}
],
"gene_symbol": "GTPBP3",
"gene_hgnc_id": 14880,
"dbsnp": "rs886037735",
"frequency_reference_population": 6.8420417e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84204e-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": 0.9624670743942261,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.27000001072883606,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.796,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.5838,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.225,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.27,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_133644.4",
"gene_symbol": "GTPBP3",
"hgnc_id": 14880,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1105G>C",
"hgvs_p": "p.Asp369His"
}
],
"clinvar_disease": "Combined oxidative phosphorylation defect type 23",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Combined oxidative phosphorylation defect type 23",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}