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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: 3-180984690-CT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=180984690&ref=CT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 180984690,
"ref": "CT",
"alt": "C",
"effect": "frameshift_variant",
"transcript": "ENST00000382564.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.300delA",
"hgvs_p": "p.Ala101fs",
"transcript": "NM_145261.4",
"protein_id": "NP_660304.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 116,
"cds_start": 300,
"cds_end": null,
"cds_length": 351,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 1416,
"mane_select": "ENST00000382564.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.300delA",
"hgvs_p": "p.Ala101fs",
"transcript": "ENST00000382564.8",
"protein_id": "ENSP00000372005.2",
"transcript_support_level": 1,
"aa_start": 100,
"aa_end": null,
"aa_length": 116,
"cds_start": 300,
"cds_end": null,
"cds_length": 351,
"cdna_start": 434,
"cdna_end": null,
"cdna_length": 1416,
"mane_select": "NM_145261.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.225delA",
"hgvs_p": "p.Ala76fs",
"transcript": "NM_001190233.2",
"protein_id": "NP_001177162.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 91,
"cds_start": 225,
"cds_end": null,
"cds_length": 276,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 1786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.225delA",
"hgvs_p": "p.Ala76fs",
"transcript": "ENST00000479269.5",
"protein_id": "ENSP00000419191.1",
"transcript_support_level": 3,
"aa_start": 75,
"aa_end": null,
"aa_length": 91,
"cds_start": 225,
"cds_end": null,
"cds_length": 276,
"cdna_start": 484,
"cdna_end": null,
"cdna_length": 610,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.225delA",
"hgvs_p": "p.Ala76fs",
"transcript": "ENST00000491873.5",
"protein_id": "ENSP00000420767.1",
"transcript_support_level": 2,
"aa_start": 75,
"aa_end": null,
"aa_length": 91,
"cds_start": 225,
"cds_end": null,
"cds_length": 276,
"cdna_start": 356,
"cdna_end": null,
"cdna_length": 769,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.45delA",
"hgvs_p": "p.Ala16fs",
"transcript": "ENST00000646965.1",
"protein_id": "ENSP00000496456.1",
"transcript_support_level": null,
"aa_start": 15,
"aa_end": null,
"aa_length": 31,
"cds_start": 45,
"cds_end": null,
"cds_length": 96,
"cdna_start": 159,
"cdna_end": null,
"cdna_length": 324,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.*76delA",
"hgvs_p": null,
"transcript": "ENST00000469657.5",
"protein_id": "ENSP00000418058.1",
"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": 1239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.2413delA",
"hgvs_p": null,
"transcript": "ENST00000482363.2",
"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": 3407,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.3622delA",
"hgvs_p": null,
"transcript": "ENST00000485675.2",
"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": 3748,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.*76delA",
"hgvs_p": null,
"transcript": "ENST00000643241.1",
"protein_id": "ENSP00000496401.1",
"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": 520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.382delA",
"hgvs_p": null,
"transcript": "NR_033721.2",
"protein_id": null,
"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": 1364,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.354delA",
"hgvs_p": null,
"transcript": "NR_033722.2",
"protein_id": null,
"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": 1336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.417delA",
"hgvs_p": null,
"transcript": "NR_033723.1",
"protein_id": null,
"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": 1399,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.266delA",
"hgvs_p": null,
"transcript": "NR_046073.1",
"protein_id": null,
"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": 1248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.*1227delA",
"hgvs_p": null,
"transcript": "ENST00000688055.1",
"protein_id": "ENSP00000508688.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 95,
"cds_start": -4,
"cds_end": null,
"cds_length": 288,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2423,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "c.*65delA",
"hgvs_p": null,
"transcript": "ENST00000486355.1",
"protein_id": "ENSP00000419991.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 59,
"cds_start": -4,
"cds_end": null,
"cds_length": 180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.*76delA",
"hgvs_p": null,
"transcript": "ENST00000469657.5",
"protein_id": "ENSP00000418058.1",
"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": 1239,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"hgvs_c": "n.*76delA",
"hgvs_p": null,
"transcript": "ENST00000643241.1",
"protein_id": "ENSP00000496401.1",
"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": 520,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAJC19",
"gene_hgnc_id": 30528,
"dbsnp": "rs587777224",
"frequency_reference_population": 0.000034202447,
"hom_count_reference_population": 0,
"allele_count_reference_population": 55,
"gnomad_exomes_af": 0.0000302177,
"gnomad_genomes_af": 0.0000723818,
"gnomad_exomes_ac": 44,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 2.322,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": 7,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5",
"acmg_by_gene": [
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000382564.8",
"gene_symbol": "DNAJC19",
"hgnc_id": 30528,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.300delA",
"hgvs_p": "p.Ala101fs"
}
],
"clinvar_disease": "3-methylglutaconic aciduria type 5",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "3-methylglutaconic aciduria type 5",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}