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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: 5-131187113-A-AG (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=131187113&ref=A&alt=AG&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "LYRM7",
"hgnc_id": 28072,
"hgvs_c": "c.244+5dupG",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_181705.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3",
"PP5"
],
"effects": [
"intron_variant"
],
"gene_symbol": "HINT1",
"hgnc_id": 4912,
"hgvs_c": "n.109-15381_109-15380insC",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "ENST00000506207.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5",
"acmg_score": 4,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "AG",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "5",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Mitochondrial complex III deficiency nuclear type 8",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 104,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6219,
"cdna_start": null,
"cds_end": null,
"cds_length": 315,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_181705.4",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.244+5dupG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000379380.9",
"protein_coding": true,
"protein_id": "NP_859056.2",
"strand": true,
"transcript": "NM_181705.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 104,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6219,
"cdna_start": null,
"cds_end": null,
"cds_length": 315,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000379380.9",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.244+4_244+5insG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_181705.4",
"protein_coding": true,
"protein_id": "ENSP00000368688.4",
"strand": true,
"transcript": "ENST00000379380.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 103,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2117,
"cdna_start": null,
"cds_end": null,
"cds_length": 312,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000855899.1",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.241+4_241+5insG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525958.1",
"strand": true,
"transcript": "ENST00000855899.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 102,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 819,
"cdna_start": null,
"cds_end": null,
"cds_length": 309,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931593.1",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.238+4_238+5insG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601652.1",
"strand": true,
"transcript": "ENST00000931593.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 101,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1601,
"cdna_start": null,
"cds_end": null,
"cds_length": 306,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931592.1",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.235+4_235+5insG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601651.1",
"strand": true,
"transcript": "ENST00000931592.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 100,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 775,
"cdna_start": null,
"cds_end": null,
"cds_length": 303,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931594.1",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.232+4_232+5insG",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601653.1",
"strand": true,
"transcript": "ENST00000931594.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 63,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6137,
"cdna_start": null,
"cds_end": null,
"cds_length": 192,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001293735.2",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.162+4815dupG",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001280664.1",
"strand": true,
"transcript": "NM_001293735.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 63,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 317,
"cdna_start": null,
"cds_end": null,
"cds_length": 192,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000507584.1",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.162+4814_162+4815insG",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423991.1",
"strand": true,
"transcript": "ENST00000507584.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 56,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1981,
"cdna_start": null,
"cds_end": null,
"cds_length": 171,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000855898.1",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.100+4_100+5insG",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000525957.1",
"strand": true,
"transcript": "ENST00000855898.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 53,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 604,
"cdna_start": null,
"cds_end": null,
"cds_length": 162,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000510516.5",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "c.91+6946_91+6947insG",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423283.1",
"strand": true,
"transcript": "ENST00000510516.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 479,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000506207.2",
"gene_hgnc_id": 4912,
"gene_symbol": "HINT1",
"hgvs_c": "n.109-15381_109-15380insC",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000506207.2",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 6066,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_121658.2",
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"hgvs_c": "n.168+6947dupG",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_121658.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs869025602",
"effect": "splice_region_variant,intron_variant",
"frequency_reference_population": null,
"gene_hgnc_id": 28072,
"gene_symbol": "LYRM7",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Mitochondrial complex III deficiency nuclear type 8",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.966,
"pos": 131187113,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.7599999904632568,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.76,
"transcript": "NM_181705.4"
}
]
}