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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: 5-179820939-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=179820939&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 179820939,
"ref": "G",
"alt": "C",
"effect": "start_lost",
"transcript": "NM_003900.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.3G>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_003900.5",
"protein_id": "NP_003891.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 440,
"cds_start": 3,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 35,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "ENST00000389805.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.3G>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000389805.9",
"protein_id": "ENSP00000374455.4",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 440,
"cds_start": 3,
"cds_end": null,
"cds_length": 1323,
"cdna_start": 35,
"cdna_end": null,
"cdna_length": 2840,
"mane_select": "NM_003900.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"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": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.3G>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000510187.5",
"protein_id": "ENSP00000424477.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 378,
"cds_start": 3,
"cds_end": null,
"cds_length": 1137,
"cdna_start": 19,
"cdna_end": null,
"cdna_length": 1714,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"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": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.3G>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000504627.1",
"protein_id": "ENSP00000425957.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 189,
"cds_start": 3,
"cds_end": null,
"cds_length": 570,
"cdna_start": 35,
"cdna_end": null,
"cdna_length": 602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"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": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.3G>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000626660.1",
"protein_id": "ENSP00000487071.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 73,
"cds_start": 3,
"cds_end": null,
"cds_length": 222,
"cdna_start": 55,
"cdna_end": null,
"cdna_length": 274,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "n.3G>C",
"hgvs_p": null,
"transcript": "ENST00000453046.5",
"protein_id": "ENSP00000405061.1",
"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": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "n.3G>C",
"hgvs_p": null,
"transcript": "ENST00000508284.5",
"protein_id": "ENSP00000424195.1",
"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": 578,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.-47-2019G>C",
"hgvs_p": null,
"transcript": "NM_001142298.2",
"protein_id": "NP_001135770.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 356,
"cds_start": -4,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2911,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 2,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.-47-2019G>C",
"hgvs_p": null,
"transcript": "NM_001142299.2",
"protein_id": "NP_001135771.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 356,
"cds_start": -4,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"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": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.-47-2019G>C",
"hgvs_p": null,
"transcript": "ENST00000514093.5",
"protein_id": "ENSP00000427308.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 166,
"cds_start": -4,
"cds_end": null,
"cds_length": 502,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 842,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.-48+1902G>C",
"hgvs_p": null,
"transcript": "ENST00000422245.5",
"protein_id": "ENSP00000394534.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 139,
"cds_start": -4,
"cds_end": null,
"cds_length": 421,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "n.100+233G>C",
"hgvs_p": null,
"transcript": "ENST00000464493.5",
"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": 532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "n.355+552G>C",
"hgvs_p": null,
"transcript": "ENST00000481335.5",
"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": 562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000301422",
"gene_hgnc_id": null,
"hgvs_c": "n.175+25C>G",
"hgvs_p": null,
"transcript": "ENST00000778815.1",
"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": 1362,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"dbsnp": "rs1309887153",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9854303598403931,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.295,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.258,
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "NM_003900.5",
"gene_symbol": "SQSTM1",
"hgnc_id": 11280,
"effects": [
"start_lost"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3G>C",
"hgvs_p": "p.Met1?"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000778815.1",
"gene_symbol": "ENSG00000301422",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.175+25C>G",
"hgvs_p": null
}
],
"clinvar_disease": " early-onset,Frontotemporal dementia and/or amyotrophic lateral sclerosis 1,Paget disease of bone 2",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Paget disease of bone 2, early-onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 1",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}