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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: 2-190205149-T-TA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=190205149&ref=T&alt=TA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 190205149,
"ref": "T",
"alt": "TA",
"effect": "frameshift_variant",
"transcript": "ENST00000359678.10",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "F?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.1128dupT",
"hgvs_p": "p.Lys377fs",
"transcript": "NM_014362.4",
"protein_id": "NP_055177.2",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 386,
"cds_start": 1128,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 2434,
"mane_select": "ENST00000359678.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F?",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.1128dupT",
"hgvs_p": "p.Lys377fs",
"transcript": "ENST00000359678.10",
"protein_id": "ENSP00000352706.5",
"transcript_support_level": 1,
"aa_start": 376,
"aa_end": null,
"aa_length": 386,
"cds_start": 1128,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 2434,
"mane_select": "NM_014362.4",
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.*77dupT",
"hgvs_p": null,
"transcript": "ENST00000392332.7",
"protein_id": "ENSP00000376144.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 338,
"cds_start": -4,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2463,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.459dupT",
"hgvs_p": "p.Lys154fs",
"transcript": "ENST00000410045.5",
"protein_id": "ENSP00000386274.1",
"transcript_support_level": 3,
"aa_start": 153,
"aa_end": null,
"aa_length": 163,
"cds_start": 459,
"cds_end": null,
"cds_length": 492,
"cdna_start": 719,
"cdna_end": null,
"cdna_length": 854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.81dupT",
"hgvs_p": "p.Lys28fs",
"transcript": "ENST00000399855.2",
"protein_id": "ENSP00000398060.1",
"transcript_support_level": 3,
"aa_start": 27,
"aa_end": null,
"aa_length": 37,
"cds_start": 81,
"cds_end": null,
"cds_length": 114,
"cdna_start": 83,
"cdna_end": null,
"cdna_length": 396,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.1128dupT",
"hgvs_p": "p.Lys377fs",
"transcript": "XM_011510953.3",
"protein_id": "XP_011509255.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 386,
"cds_start": 1128,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 1423,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.1128dupT",
"hgvs_p": "p.Lys377fs",
"transcript": "XM_047443905.1",
"protein_id": "XP_047299861.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 386,
"cds_start": 1128,
"cds_end": null,
"cds_length": 1161,
"cdna_start": 1204,
"cdna_end": null,
"cdna_length": 15408,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "F",
"aa_alt": "F?",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.630dupT",
"hgvs_p": "p.Lys211fs",
"transcript": "XM_011510954.2",
"protein_id": "XP_011509256.1",
"transcript_support_level": null,
"aa_start": 210,
"aa_end": null,
"aa_length": 220,
"cds_start": 630,
"cds_end": null,
"cds_length": 663,
"cdna_start": 828,
"cdna_end": null,
"cdna_length": 2058,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "n.363dupT",
"hgvs_p": null,
"transcript": "ENST00000486981.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 581,
"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": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "n.1170dupT",
"hgvs_p": null,
"transcript": "XR_922903.3",
"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": 1389,
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"hgvs_c": "c.*77dupT",
"hgvs_p": null,
"transcript": "NM_198047.3",
"protein_id": "NP_932164.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 338,
"cds_start": -4,
"cds_end": null,
"cds_length": 1017,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2400,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HIBCH",
"gene_hgnc_id": 4908,
"dbsnp": "rs863225062",
"frequency_reference_population": 6.869774e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.86977e-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": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0,
"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": 2.135,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1_Moderate,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1_Moderate",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000359678.10",
"gene_symbol": "HIBCH",
"hgnc_id": 4908,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1128dupT",
"hgvs_p": "p.Lys377fs"
}
],
"clinvar_disease": "3-hydroxyisobutyryl-CoA hydrolase deficiency,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:2",
"phenotype_combined": "3-hydroxyisobutyryl-CoA hydrolase deficiency|not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}