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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: 5-179825182-TGAA-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=179825182&ref=TGAA&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM4_Supporting"
],
"effects": [
"disruptive_inframe_deletion"
],
"gene_symbol": "SQSTM1",
"hgnc_id": 11280,
"hgvs_c": "c.714_716delGAA",
"hgvs_p": "p.Lys238del",
"inheritance_mode": "AD,AR",
"pathogenic_score": 1,
"score": 1,
"transcript": "NM_003900.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4_Supporting",
"acmg_score": 1,
"allele_count_reference_population": 41,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " early-onset,Frontotemporal dementia and/or amyotrophic lateral sclerosis 1,Frontotemporal dementia and/or amyotrophic lateral sclerosis 3,Paget disease of bone 2,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 440,
"aa_ref": "KN",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2840,
"cdna_start": 746,
"cds_end": null,
"cds_length": 1323,
"cds_start": 714,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_003900.5",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.714_716delGAA",
"hgvs_p": "p.Lys238del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000389805.9",
"protein_coding": true,
"protein_id": "NP_003891.1",
"strand": true,
"transcript": "NM_003900.5",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 440,
"aa_ref": "KN",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2840,
"cdna_start": 746,
"cds_end": null,
"cds_length": 1323,
"cds_start": 714,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000389805.9",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.714_716delGAA",
"hgvs_p": "p.Lys238del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003900.5",
"protein_coding": true,
"protein_id": "ENSP00000374455.4",
"strand": true,
"transcript": "ENST00000389805.9",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 356,
"aa_ref": "KN",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2253,
"cdna_start": 982,
"cds_end": null,
"cds_length": 1071,
"cds_start": 462,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 7,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000360718.5",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.462_464delGAA",
"hgvs_p": "p.Lys154del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000353944.5",
"strand": true,
"transcript": "ENST00000360718.5",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 448,
"aa_ref": "KN",
"aa_start": 246,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2043,
"cdna_start": 773,
"cds_end": null,
"cds_length": 1347,
"cds_start": 738,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000884700.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.738_740delGAA",
"hgvs_p": "p.Lys246del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554759.1",
"strand": true,
"transcript": "ENST00000884700.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 438,
"aa_ref": "KN",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2881,
"cdna_start": 793,
"cds_end": null,
"cds_length": 1317,
"cds_start": 714,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000884698.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.714_716delGAA",
"hgvs_p": "p.Lys238del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554757.1",
"strand": true,
"transcript": "ENST00000884698.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 437,
"aa_ref": "KN",
"aa_start": 235,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2001,
"cdna_start": 735,
"cds_end": null,
"cds_length": 1314,
"cds_start": 705,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000951526.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.705_707delGAA",
"hgvs_p": "p.Lys235del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621585.1",
"strand": true,
"transcript": "ENST00000951526.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 402,
"aa_ref": "KN",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1904,
"cdna_start": 749,
"cds_end": null,
"cds_length": 1209,
"cds_start": 714,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000884703.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.714_716delGAA",
"hgvs_p": "p.Lys238del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554762.1",
"strand": true,
"transcript": "ENST00000884703.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 378,
"aa_ref": "KN",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1714,
"cdna_start": 730,
"cds_end": null,
"cds_length": 1137,
"cds_start": 714,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000510187.5",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.714_716delGAA",
"hgvs_p": "p.Lys238del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000424477.1",
"strand": true,
"transcript": "ENST00000510187.5",
"transcript_support_level": 5
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 356,
"aa_ref": "KN",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2911,
"cdna_start": 817,
"cds_end": null,
"cds_length": 1071,
"cds_start": 462,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001142298.2",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.462_464delGAA",
"hgvs_p": "p.Lys154del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135770.1",
"strand": true,
"transcript": "NM_001142298.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 356,
"aa_ref": "KN",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2827,
"cdna_start": 733,
"cds_end": null,
"cds_length": 1071,
"cds_start": 462,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 9,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001142299.2",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.462_464delGAA",
"hgvs_p": "p.Lys154del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001135771.1",
"strand": true,
"transcript": "NM_001142299.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 303,
"aa_ref": "KN",
"aa_start": 238,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1605,
"cdna_start": 748,
"cds_end": null,
"cds_length": 912,
"cds_start": 714,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000884704.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.714_716delGAA",
"hgvs_p": "p.Lys238del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554763.1",
"strand": true,
"transcript": "ENST00000884704.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 166,
"aa_ref": "KN",
"aa_start": 154,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 842,
"cdna_start": 802,
"cds_end": null,
"cds_length": 502,
"cds_start": 462,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000514093.5",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.462_464delGAA",
"hgvs_p": "p.Lys154del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000427308.1",
"strand": true,
"transcript": "ENST00000514093.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 413,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1938,
"cdna_start": null,
"cds_end": null,
"cds_length": 1242,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000884702.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.673+863_673+865delGAA",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554761.1",
"strand": true,
"transcript": "ENST00000884702.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 289,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2390,
"cdna_start": null,
"cds_end": null,
"cds_length": 870,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000884699.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.301+2133_301+2135delGAA",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554758.1",
"strand": true,
"transcript": "ENST00000884699.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 257,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1470,
"cdna_start": null,
"cds_end": null,
"cds_length": 774,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000884701.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.205+4045_205+4047delGAA",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554760.1",
"strand": true,
"transcript": "ENST00000884701.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 255,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1455,
"cdna_start": null,
"cds_end": null,
"cds_length": 768,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000951527.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.205+4045_205+4047delGAA",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000621586.1",
"strand": true,
"transcript": "ENST00000951527.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 120,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1051,
"cdna_start": null,
"cds_end": null,
"cds_length": 363,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000884705.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "c.205+4045_205+4047delGAA",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000554764.1",
"strand": true,
"transcript": "ENST00000884705.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 808,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000466342.1",
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"hgvs_c": "n.413_415delGAA",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000466342.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs796052214",
"effect": "disruptive_inframe_deletion",
"frequency_reference_population": 0.000025402254,
"gene_hgnc_id": 11280,
"gene_symbol": "SQSTM1",
"gnomad_exomes_ac": 39,
"gnomad_exomes_af": 0.0000266797,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131366,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Frontotemporal dementia and/or amyotrophic lateral sclerosis 3|Paget disease of bone 2, early-onset;Frontotemporal dementia and/or amyotrophic lateral sclerosis 1|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.408,
"pos": 179825182,
"ref": "TGAA",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05999999865889549,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.06,
"transcript": "NM_003900.5"
}
]
}