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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: 3-119498734-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=119498734&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 119498734,
"ref": "A",
"alt": "G",
"effect": "start_lost",
"transcript": "NM_016589.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_016589.4",
"protein_id": "NP_057673.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 285,
"cds_start": 1,
"cds_end": null,
"cds_length": 858,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000494664.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016589.4"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000494664.6",
"protein_id": "ENSP00000418803.1",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 285,
"cds_start": 1,
"cds_end": null,
"cds_length": 858,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016589.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494664.6"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.1A>G",
"hgvs_p": null,
"transcript": "ENST00000264244.7",
"protein_id": "ENSP00000264244.3",
"transcript_support_level": 1,
"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": "ENST00000264244.7"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000854204.1",
"protein_id": "ENSP00000524263.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 284,
"cds_start": 1,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854204.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000854206.1",
"protein_id": "ENSP00000524265.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 255,
"cds_start": 1,
"cds_end": null,
"cds_length": 768,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854206.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000854205.1",
"protein_id": "ENSP00000524264.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 248,
"cds_start": 1,
"cds_end": null,
"cds_length": 747,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000854205.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_001438040.1",
"protein_id": "NP_001424969.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 151,
"cds_start": 1,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438040.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000493694.1",
"protein_id": "ENSP00000419510.1",
"transcript_support_level": 2,
"aa_start": 1,
"aa_end": null,
"aa_length": 151,
"cds_start": 1,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000493694.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000466984.1",
"protein_id": "ENSP00000420122.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 149,
"cds_start": 1,
"cds_end": null,
"cds_length": 452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000466984.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000935160.1",
"protein_id": "ENSP00000605219.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 114,
"cds_start": 1,
"cds_end": null,
"cds_length": 345,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000935160.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.1A>G",
"hgvs_p": null,
"transcript": "ENST00000463927.6",
"protein_id": "ENSP00000417205.2",
"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": "ENST00000463927.6"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.1A>G",
"hgvs_p": null,
"transcript": "ENST00000486418.5",
"protein_id": "ENSP00000417083.1",
"transcript_support_level": 3,
"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": "ENST00000486418.5"
},
{
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.1A>G",
"hgvs_p": null,
"transcript": "ENST00000492164.5",
"protein_id": "ENSP00000418846.1",
"transcript_support_level": 3,
"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": "ENST00000492164.5"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.-84A>G",
"hgvs_p": null,
"transcript": "ENST00000498399.1",
"protein_id": "ENSP00000420812.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000498399.1"
}
],
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"dbsnp": "rs773031917",
"frequency_reference_population": 0.0000043370883,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000273642,
"gnomad_genomes_af": 0.0000197083,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5235844850540161,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.185,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.12,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.452,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_016589.4",
"gene_symbol": "TIMMDC1",
"hgnc_id": 1321,
"effects": [
"start_lost"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?"
}
],
"clinvar_disease": " nuclear type 31,Mitochondrial complex I deficiency",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Mitochondrial complex I deficiency, nuclear type 31",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}