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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: 5-179833040-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=179833040&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 179833040,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003900.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.763G>C",
"hgvs_p": "p.Val255Leu",
"transcript": "NM_003900.5",
"protein_id": "NP_003891.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 440,
"cds_start": 763,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000389805.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003900.5"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.763G>C",
"hgvs_p": "p.Val255Leu",
"transcript": "ENST00000389805.9",
"protein_id": "ENSP00000374455.4",
"transcript_support_level": 1,
"aa_start": 255,
"aa_end": null,
"aa_length": 440,
"cds_start": 763,
"cds_end": null,
"cds_length": 1323,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003900.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389805.9"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.511G>C",
"hgvs_p": "p.Val171Leu",
"transcript": "ENST00000360718.5",
"protein_id": "ENSP00000353944.5",
"transcript_support_level": 1,
"aa_start": 171,
"aa_end": null,
"aa_length": 356,
"cds_start": 511,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000360718.5"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.787G>C",
"hgvs_p": "p.Val263Leu",
"transcript": "ENST00000884700.1",
"protein_id": "ENSP00000554759.1",
"transcript_support_level": null,
"aa_start": 263,
"aa_end": null,
"aa_length": 448,
"cds_start": 787,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884700.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.763G>C",
"hgvs_p": "p.Val255Leu",
"transcript": "ENST00000884698.1",
"protein_id": "ENSP00000554757.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 438,
"cds_start": 763,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884698.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.754G>C",
"hgvs_p": "p.Val252Leu",
"transcript": "ENST00000951526.1",
"protein_id": "ENSP00000621585.1",
"transcript_support_level": null,
"aa_start": 252,
"aa_end": null,
"aa_length": 437,
"cds_start": 754,
"cds_end": null,
"cds_length": 1314,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951526.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.682G>C",
"hgvs_p": "p.Val228Leu",
"transcript": "ENST00000884702.1",
"protein_id": "ENSP00000554761.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 413,
"cds_start": 682,
"cds_end": null,
"cds_length": 1242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884702.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.763G>C",
"hgvs_p": "p.Val255Leu",
"transcript": "ENST00000884703.1",
"protein_id": "ENSP00000554762.1",
"transcript_support_level": null,
"aa_start": 255,
"aa_end": null,
"aa_length": 402,
"cds_start": 763,
"cds_end": null,
"cds_length": 1209,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884703.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.763G>C",
"hgvs_p": "p.Val255Leu",
"transcript": "ENST00000510187.5",
"protein_id": "ENSP00000424477.1",
"transcript_support_level": 5,
"aa_start": 255,
"aa_end": null,
"aa_length": 378,
"cds_start": 763,
"cds_end": null,
"cds_length": 1137,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000510187.5"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.511G>C",
"hgvs_p": "p.Val171Leu",
"transcript": "NM_001142298.2",
"protein_id": "NP_001135770.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 356,
"cds_start": 511,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142298.2"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.511G>C",
"hgvs_p": "p.Val171Leu",
"transcript": "NM_001142299.2",
"protein_id": "NP_001135771.1",
"transcript_support_level": null,
"aa_start": 171,
"aa_end": null,
"aa_length": 356,
"cds_start": 511,
"cds_end": null,
"cds_length": 1071,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142299.2"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.310G>C",
"hgvs_p": "p.Val104Leu",
"transcript": "ENST00000884699.1",
"protein_id": "ENSP00000554758.1",
"transcript_support_level": null,
"aa_start": 104,
"aa_end": null,
"aa_length": 289,
"cds_start": 310,
"cds_end": null,
"cds_length": 870,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884699.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.214G>C",
"hgvs_p": "p.Val72Leu",
"transcript": "ENST00000884701.1",
"protein_id": "ENSP00000554760.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 257,
"cds_start": 214,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884701.1"
},
{
"aa_ref": "V",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.214G>C",
"hgvs_p": "p.Val72Leu",
"transcript": "ENST00000951527.1",
"protein_id": "ENSP00000621586.1",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 255,
"cds_start": 214,
"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": "ENST00000951527.1"
},
{
"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": 5,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.755-3396G>C",
"hgvs_p": null,
"transcript": "ENST00000884704.1",
"protein_id": "ENSP00000554763.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 303,
"cds_start": null,
"cds_end": null,
"cds_length": 912,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884704.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "c.206-3396G>C",
"hgvs_p": null,
"transcript": "ENST00000884705.1",
"protein_id": "ENSP00000554764.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 120,
"cds_start": null,
"cds_end": null,
"cds_length": 363,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884705.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "SQSTM1",
"gene_hgnc_id": 11280,
"hgvs_c": "n.462G>C",
"hgvs_p": null,
"transcript": "ENST00000466342.1",
"protein_id": null,
"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": "retained_intron",
"feature": "ENST00000466342.1"
}
],
"gene_symbol": "SQSTM1",
"gene_hgnc_id": 11280,
"dbsnp": "rs182522590",
"frequency_reference_population": 0.000019204726,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000191534,
"gnomad_genomes_af": 0.0000196969,
"gnomad_exomes_ac": 28,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.27235525846481323,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.524,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.981,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.02,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 9.722,
"phylop100way_prediction": "Pathogenic",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BP6,BS1",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS1"
],
"verdict": "Likely_benign",
"transcript": "NM_003900.5",
"gene_symbol": "SQSTM1",
"hgnc_id": 11280,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.763G>C",
"hgvs_p": "p.Val255Leu"
}
],
"clinvar_disease": " early-onset,Frontotemporal dementia and/or amyotrophic lateral sclerosis 1,Paget disease of bone 2,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Paget disease of bone 2, early-onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 1|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}