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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: 5-131187053-A-AATT (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=131187053&ref=A&alt=AATT&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 131187053,
"ref": "A",
"alt": "AATT",
"effect": "conservative_inframe_insertion",
"transcript": "ENST00000379380.9",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "LL",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM7",
"gene_hgnc_id": 28072,
"hgvs_c": "c.193_195dupTTA",
"hgvs_p": "p.Leu66dup",
"transcript": "NM_181705.4",
"protein_id": "NP_859056.2",
"transcript_support_level": null,
"aa_start": 66,
"aa_end": null,
"aa_length": 104,
"cds_start": 196,
"cds_end": null,
"cds_length": 315,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 6219,
"mane_select": "ENST00000379380.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "LL",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_insertion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LYRM7",
"gene_hgnc_id": 28072,
"hgvs_c": "c.193_195dupTTA",
"hgvs_p": "p.Leu66dup",
"transcript": "ENST00000379380.9",
"protein_id": "ENSP00000368688.4",
"transcript_support_level": 1,
"aa_start": 66,
"aa_end": null,
"aa_length": 104,
"cds_start": 196,
"cds_end": null,
"cds_length": 315,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 6219,
"mane_select": "NM_181705.4",
"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": 3,
"intron_rank_end": null,
"gene_symbol": "LYRM7",
"gene_hgnc_id": 28072,
"hgvs_c": "c.162+4759_162+4761dupTTA",
"hgvs_p": null,
"transcript": "NM_001293735.2",
"protein_id": "NP_001280664.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 63,
"cds_start": -4,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6137,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "LYRM7",
"gene_hgnc_id": 28072,
"hgvs_c": "c.162+4759_162+4761dupTTA",
"hgvs_p": null,
"transcript": "ENST00000507584.1",
"protein_id": "ENSP00000423991.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 63,
"cds_start": -4,
"cds_end": null,
"cds_length": 192,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 317,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LYRM7",
"gene_hgnc_id": 28072,
"hgvs_c": "c.91+6891_91+6893dupTTA",
"hgvs_p": null,
"transcript": "ENST00000510516.5",
"protein_id": "ENSP00000423283.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 53,
"cds_start": -4,
"cds_end": null,
"cds_length": 162,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 604,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HINT1",
"gene_hgnc_id": 4912,
"hgvs_c": "n.109-15323_109-15321dupAAT",
"hgvs_p": null,
"transcript": "ENST00000506207.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 479,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "LYRM7",
"gene_hgnc_id": 28072,
"hgvs_c": "n.168+6891_168+6893dupTTA",
"hgvs_p": null,
"transcript": "NR_121658.2",
"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": 6066,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LYRM7",
"gene_hgnc_id": 28072,
"dbsnp": "rs869025603",
"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": 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": 4.121,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PM4_Supporting,PP5",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PM4_Supporting",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000379380.9",
"gene_symbol": "LYRM7",
"hgnc_id": 28072,
"effects": [
"conservative_inframe_insertion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.193_195dupTTA",
"hgvs_p": "p.Leu66dup"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000506207.2",
"gene_symbol": "HINT1",
"hgnc_id": 4912,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.109-15323_109-15321dupAAT",
"hgvs_p": null
}
],
"clinvar_disease": "Mitochondrial complex III deficiency nuclear type 8",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Mitochondrial complex III deficiency nuclear type 8",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}