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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: 16-4337142-T-TGGGCCCTGGGCTGCC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=4337142&ref=T&alt=TGGGCCCTGGGCTGCC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 4337142,
"ref": "T",
"alt": "TGGGCCCTGGGCTGCC",
"effect": "disruptive_inframe_insertion",
"transcript": "ENST00000433375.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "PGPGLP",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS2",
"gene_hgnc_id": 29450,
"hgvs_c": "c.1194_1208dupGGGCCCTGGGCTGCC",
"hgvs_p": "p.Pro403_Gly404insGlyProGlyLeuPro",
"transcript": "NM_032575.3",
"protein_id": "NP_115964.2",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 524,
"cds_start": 1209,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1463,
"cdna_end": null,
"cdna_length": 3900,
"mane_select": "ENST00000433375.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PGPGLP",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS2",
"gene_hgnc_id": 29450,
"hgvs_c": "c.1194_1208dupGGGCCCTGGGCTGCC",
"hgvs_p": "p.Pro403_Gly404insGlyProGlyLeuPro",
"transcript": "ENST00000433375.2",
"protein_id": "ENSP00000395547.1",
"transcript_support_level": 1,
"aa_start": 403,
"aa_end": null,
"aa_length": 524,
"cds_start": 1209,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 1463,
"cdna_end": null,
"cdna_length": 3900,
"mane_select": "NM_032575.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PGPGLP",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS2",
"gene_hgnc_id": 29450,
"hgvs_c": "c.1194_1208dupGGGCCCTGGGCTGCC",
"hgvs_p": "p.Pro403_Gly404insGlyProGlyLeuPro",
"transcript": "NM_001318918.2",
"protein_id": "NP_001305847.1",
"transcript_support_level": null,
"aa_start": 403,
"aa_end": null,
"aa_length": 524,
"cds_start": 1209,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 2030,
"cdna_end": null,
"cdna_length": 4467,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "PGPGLP",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLIS2",
"gene_hgnc_id": 29450,
"hgvs_c": "c.1194_1208dupGGGCCCTGGGCTGCC",
"hgvs_p": "p.Pro403_Gly404insGlyProGlyLeuPro",
"transcript": "ENST00000262366.7",
"protein_id": "ENSP00000262366.3",
"transcript_support_level": 2,
"aa_start": 403,
"aa_end": null,
"aa_length": 524,
"cds_start": 1209,
"cds_end": null,
"cds_length": 1575,
"cdna_start": 2030,
"cdna_end": null,
"cdna_length": 4469,
"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": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000262712",
"gene_hgnc_id": null,
"hgvs_c": "n.662_676dupGGCAGCCCAGGGCCC",
"hgvs_p": null,
"transcript": "ENST00000574705.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 1949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PAM16",
"gene_hgnc_id": 29679,
"hgvs_c": "c.291+3763_291+3777dupGGCAGCCCAGGGCCC",
"hgvs_p": null,
"transcript": "ENST00000577031.5",
"protein_id": "ENSP00000459113.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 129,
"cds_start": -4,
"cds_end": null,
"cds_length": 390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 548,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GLIS2",
"gene_hgnc_id": 29450,
"dbsnp": "rs878855164",
"frequency_reference_population": 0.0000021659744,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000216597,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"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": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.06,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000433375.2",
"gene_symbol": "GLIS2",
"hgnc_id": 29450,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1194_1208dupGGGCCCTGGGCTGCC",
"hgvs_p": "p.Pro403_Gly404insGlyProGlyLeuPro"
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000574705.1",
"gene_symbol": "ENSG00000262712",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.662_676dupGGCAGCCCAGGGCCC",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "ENST00000577031.5",
"gene_symbol": "PAM16",
"hgnc_id": 29679,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.291+3763_291+3777dupGGCAGCCCAGGGCCC",
"hgvs_p": null
}
],
"clinvar_disease": "Nephronophthisis",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Nephronophthisis",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}