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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: 4-125434258-G-GACTGGA (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=125434258&ref=G&alt=GACTGGA&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 125434258,
"ref": "G",
"alt": "GACTGGA",
"effect": "disruptive_inframe_insertion",
"transcript": "NM_001291303.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.7041_7046dupTGGAAC",
"hgvs_p": "p.Thr2349_Ile2350insGlyThr",
"transcript": "NM_001291303.3",
"protein_id": "NP_001278232.1",
"transcript_support_level": null,
"aa_start": 2349,
"aa_end": null,
"aa_length": 4983,
"cds_start": 7047,
"cds_end": null,
"cds_length": 14952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000394329.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291303.3"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.7041_7046dupTGGAAC",
"hgvs_p": "p.Thr2349_Ile2350insGlyThr",
"transcript": "ENST00000394329.9",
"protein_id": "ENSP00000377862.4",
"transcript_support_level": 5,
"aa_start": 2349,
"aa_end": null,
"aa_length": 4983,
"cds_start": 7047,
"cds_end": null,
"cds_length": 14952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001291303.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394329.9"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.1935_1940dupTGGAAC",
"hgvs_p": "p.Thr647_Ile648insGlyThr",
"transcript": "ENST00000335110.5",
"protein_id": "ENSP00000335169.5",
"transcript_support_level": 1,
"aa_start": 647,
"aa_end": null,
"aa_length": 3222,
"cds_start": 1941,
"cds_end": null,
"cds_length": 9669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335110.5"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.7041_7046dupTGGAAC",
"hgvs_p": "p.Thr2349_Ile2350insGlyThr",
"transcript": "NM_001438396.1",
"protein_id": "NP_001425325.1",
"transcript_support_level": null,
"aa_start": 2349,
"aa_end": null,
"aa_length": 4983,
"cds_start": 7047,
"cds_end": null,
"cds_length": 14952,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438396.1"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.7041_7046dupTGGAAC",
"hgvs_p": "p.Thr2349_Ile2350insGlyThr",
"transcript": "NM_001291285.3",
"protein_id": "NP_001278214.1",
"transcript_support_level": null,
"aa_start": 2349,
"aa_end": null,
"aa_length": 4982,
"cds_start": 7047,
"cds_end": null,
"cds_length": 14949,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001291285.3"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.7041_7046dupTGGAAC",
"hgvs_p": "p.Thr2349_Ile2350insGlyThr",
"transcript": "NM_001438397.1",
"protein_id": "NP_001425326.1",
"transcript_support_level": null,
"aa_start": 2349,
"aa_end": null,
"aa_length": 4982,
"cds_start": 7047,
"cds_end": null,
"cds_length": 14949,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001438397.1"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.7041_7046dupTGGAAC",
"hgvs_p": "p.Thr2349_Ile2350insGlyThr",
"transcript": "NM_024582.6",
"protein_id": "NP_078858.4",
"transcript_support_level": null,
"aa_start": 2349,
"aa_end": null,
"aa_length": 4981,
"cds_start": 7047,
"cds_end": null,
"cds_length": 14946,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024582.6"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.1812_1817dupTGGAAC",
"hgvs_p": "p.Thr606_Ile607insGlyThr",
"transcript": "NM_001437895.1",
"protein_id": "NP_001424824.1",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 3240,
"cds_start": 1818,
"cds_end": null,
"cds_length": 9723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001437895.1"
},
{
"aa_ref": "T",
"aa_alt": "TGT",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"disruptive_inframe_insertion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"hgvs_c": "c.1812_1817dupTGGAAC",
"hgvs_p": "p.Thr606_Ile607insGlyThr",
"transcript": "ENST00000674496.2",
"protein_id": "ENSP00000501473.2",
"transcript_support_level": null,
"aa_start": 606,
"aa_end": null,
"aa_length": 3240,
"cds_start": 1818,
"cds_end": null,
"cds_length": 9723,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674496.2"
}
],
"gene_symbol": "FAT4",
"gene_hgnc_id": 23109,
"dbsnp": "rs587777724",
"frequency_reference_population": 6.848274e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84827e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"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": 7.965,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PM4,PP3,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM4",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001291303.3",
"gene_symbol": "FAT4",
"hgnc_id": 23109,
"effects": [
"disruptive_inframe_insertion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7041_7046dupTGGAAC",
"hgvs_p": "p.Thr2349_Ile2350insGlyThr"
}
],
"clinvar_disease": "Hennekam lymphangiectasia-lymphedema syndrome 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Hennekam lymphangiectasia-lymphedema syndrome 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}