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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: 5-179836542-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=179836542&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 179836542,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000389805.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.1272C>T",
"hgvs_p": "p.Ile424Ile",
"transcript": "NM_003900.5",
"protein_id": "NP_003891.1",
"transcript_support_level": null,
"aa_start": 424,
"aa_end": null,
"aa_length": 440,
"cds_start": 1272,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 1304,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "ENST00000389805.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.1272C>T",
"hgvs_p": "p.Ile424Ile",
"transcript": "ENST00000389805.9",
"protein_id": "ENSP00000374455.4",
"transcript_support_level": 1,
"aa_start": 424,
"aa_end": null,
"aa_length": 440,
"cds_start": 1272,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 1304,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "NM_003900.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.1020C>T",
"hgvs_p": "p.Ile340Ile",
"transcript": "ENST00000360718.5",
"protein_id": "ENSP00000353944.5",
"transcript_support_level": 1,
"aa_start": 340,
"aa_end": null,
"aa_length": 356,
"cds_start": 1020,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 1540,
"cdna_end": null,
"cdna_length": 2253,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRNIP",
"gene_hgnc_id": 30817,
"hgvs_c": "n.*1148G>A",
"hgvs_p": null,
"transcript": "ENST00000522663.5",
"protein_id": "ENSP00000429835.1",
"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": 2879,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRNIP",
"gene_hgnc_id": 30817,
"hgvs_c": "n.*1148G>A",
"hgvs_p": null,
"transcript": "ENST00000522663.5",
"protein_id": "ENSP00000429835.1",
"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": 2879,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.1022C>T",
"hgvs_p": "p.Ser341Leu",
"transcript": "ENST00000510187.5",
"protein_id": "ENSP00000424477.1",
"transcript_support_level": 5,
"aa_start": 341,
"aa_end": null,
"aa_length": 378,
"cds_start": 1022,
"cds_end": null,
"cds_length": 1137,
"cdna_start": 1038,
"cdna_end": null,
"cdna_length": 1714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.1020C>T",
"hgvs_p": "p.Ile340Ile",
"transcript": "NM_001142298.2",
"protein_id": "NP_001135770.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 356,
"cds_start": 1020,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 1375,
"cdna_end": null,
"cdna_length": 2911,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.1020C>T",
"hgvs_p": "p.Ile340Ile",
"transcript": "NM_001142299.2",
"protein_id": "NP_001135771.1",
"transcript_support_level": null,
"aa_start": 340,
"aa_end": null,
"aa_length": 356,
"cds_start": 1020,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 1291,
"cdna_end": null,
"cdna_length": 2827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRNIP",
"gene_hgnc_id": 30817,
"hgvs_c": "c.*636G>A",
"hgvs_p": null,
"transcript": "ENST00000518235.5",
"protein_id": "ENSP00000430298.1",
"transcript_support_level": 2,
"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": 1244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"dbsnp": "rs374985304",
"frequency_reference_population": 0.00014372962,
"hom_count_reference_population": 0,
"allele_count_reference_population": 232,
"gnomad_exomes_af": 0.000145701,
"gnomad_genomes_af": 0.000124796,
"gnomad_exomes_ac": 213,
"gnomad_genomes_ac": 19,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.035939425230026245,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.189,
"revel_prediction": "Benign",
"alphamissense_score": 0.0997,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.748,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000389805.9",
"gene_symbol": "SQSTM1",
"hgnc_id": 11280,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1272C>T",
"hgvs_p": "p.Ile424Ile"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000522663.5",
"gene_symbol": "MRNIP",
"hgnc_id": 30817,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*1148G>A",
"hgvs_p": null
}
],
"clinvar_disease": " early-onset,Frontotemporal dementia and/or amyotrophic lateral sclerosis 1,Paget disease of bone 2,SQSTM1-related disorder,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "SQSTM1-related disorder|not provided|Frontotemporal dementia and/or amyotrophic lateral sclerosis 1;Paget disease of bone 2, early-onset",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}