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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: 8-54625914-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=54625914&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 54625914,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000220676.2",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.2032C>T",
"hgvs_p": "p.Gln678*",
"transcript": "NM_006269.2",
"protein_id": "NP_006260.1",
"transcript_support_level": null,
"aa_start": 678,
"aa_end": null,
"aa_length": 2156,
"cds_start": 2032,
"cds_end": null,
"cds_length": 6471,
"cdna_start": 2151,
"cdna_end": null,
"cdna_length": 7071,
"mane_select": "ENST00000220676.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.2032C>T",
"hgvs_p": "p.Gln678*",
"transcript": "ENST00000220676.2",
"protein_id": "ENSP00000220676.1",
"transcript_support_level": 1,
"aa_start": 678,
"aa_end": null,
"aa_length": 2156,
"cds_start": 2032,
"cds_end": null,
"cds_length": 6471,
"cdna_start": 2151,
"cdna_end": null,
"cdna_length": 7071,
"mane_select": "NM_006269.2",
"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": 29,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.787+3626C>T",
"hgvs_p": null,
"transcript": "ENST00000637698.1",
"protein_id": "ENSP00000490104.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1416,
"cds_start": -4,
"cds_end": null,
"cds_length": 4251,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6177,
"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": 30,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.787+3626C>T",
"hgvs_p": null,
"transcript": "NM_001375654.1",
"protein_id": "NP_001362583.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1383,
"cds_start": -4,
"cds_end": null,
"cds_length": 4152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5592,
"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": 23,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.787+3626C>T",
"hgvs_p": null,
"transcript": "ENST00000636932.1",
"protein_id": "ENSP00000489857.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1106,
"cds_start": -4,
"cds_end": null,
"cds_length": 3321,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3649,
"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": 30,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.808+3626C>T",
"hgvs_p": null,
"transcript": "XM_047422069.1",
"protein_id": "XP_047278025.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1423,
"cds_start": -4,
"cds_end": null,
"cds_length": 4272,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5885,
"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": 30,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.808+3626C>T",
"hgvs_p": null,
"transcript": "XM_047422070.1",
"protein_id": "XP_047278026.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1422,
"cds_start": -4,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5882,
"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": 30,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.808+3626C>T",
"hgvs_p": null,
"transcript": "XM_047422071.1",
"protein_id": "XP_047278027.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1422,
"cds_start": -4,
"cds_end": null,
"cds_length": 4269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5882,
"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": 31,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.808+3626C>T",
"hgvs_p": null,
"transcript": "XM_047422072.1",
"protein_id": "XP_047278028.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1390,
"cds_start": -4,
"cds_end": null,
"cds_length": 4173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5786,
"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": 26,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.808+3626C>T",
"hgvs_p": null,
"transcript": "XM_047422073.1",
"protein_id": "XP_047278029.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1222,
"cds_start": -4,
"cds_end": null,
"cds_length": 3669,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4123,
"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": 22,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"hgvs_c": "c.808+3626C>T",
"hgvs_p": null,
"transcript": "XM_047422074.1",
"protein_id": "XP_047278030.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1021,
"cds_start": -4,
"cds_end": null,
"cds_length": 3066,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RP1",
"gene_hgnc_id": 10263,
"dbsnp": "rs878853328",
"frequency_reference_population": 6.841583e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84158e-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": 0.27000001072883606,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.068,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000220676.2",
"gene_symbol": "RP1",
"hgnc_id": 10263,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.2032C>T",
"hgvs_p": "p.Gln678*"
}
],
"clinvar_disease": "Retinal dystrophy,Retinitis pigmentosa,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"phenotype_combined": "Retinal dystrophy|not provided|Retinitis pigmentosa",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}