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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: 1-25811692-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=25811692&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 25811692,
"ref": "T",
"alt": "C",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000361547.7",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SELENON",
"gene_hgnc_id": 15999,
"hgvs_c": "c.1094T>C",
"hgvs_p": "p.Met365Thr",
"transcript": "NM_020451.3",
"protein_id": "NP_065184.2",
"transcript_support_level": null,
"aa_start": 365,
"aa_end": null,
"aa_length": 590,
"cds_start": 1094,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 1132,
"cdna_end": null,
"cdna_length": 4314,
"mane_select": "ENST00000361547.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SELENON",
"gene_hgnc_id": 15999,
"hgvs_c": "c.1094T>C",
"hgvs_p": "p.Met365Thr",
"transcript": "ENST00000361547.7",
"protein_id": "ENSP00000355141.2",
"transcript_support_level": 1,
"aa_start": 365,
"aa_end": null,
"aa_length": 590,
"cds_start": 1094,
"cds_end": null,
"cds_length": 1773,
"cdna_start": 1132,
"cdna_end": null,
"cdna_length": 4314,
"mane_select": "NM_020451.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SELENON",
"gene_hgnc_id": 15999,
"hgvs_c": "c.992T>C",
"hgvs_p": "p.Met331Thr",
"transcript": "NM_206926.2",
"protein_id": "NP_996809.1",
"transcript_support_level": null,
"aa_start": 331,
"aa_end": null,
"aa_length": 556,
"cds_start": 992,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1030,
"cdna_end": null,
"cdna_length": 4212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SELENON",
"gene_hgnc_id": 15999,
"hgvs_c": "c.992T>C",
"hgvs_p": "p.Met331Thr",
"transcript": "ENST00000374315.1",
"protein_id": "ENSP00000363434.1",
"transcript_support_level": 5,
"aa_start": 331,
"aa_end": null,
"aa_length": 556,
"cds_start": 992,
"cds_end": null,
"cds_length": 1671,
"cdna_start": 1030,
"cdna_end": null,
"cdna_length": 4212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SELENON",
"gene_hgnc_id": 15999,
"hgvs_c": "c.923T>C",
"hgvs_p": "p.Met308Thr",
"transcript": "ENST00000354177.9",
"protein_id": "ENSP00000346109.5",
"transcript_support_level": 5,
"aa_start": 308,
"aa_end": null,
"aa_length": 533,
"cds_start": 923,
"cds_end": null,
"cds_length": 1602,
"cdna_start": 923,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SELENON",
"gene_hgnc_id": 15999,
"hgvs_c": "n.992T>C",
"hgvs_p": null,
"transcript": "ENST00000494537.2",
"protein_id": "ENSP00000508308.1",
"transcript_support_level": 3,
"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": 2032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000255054",
"gene_hgnc_id": null,
"hgvs_c": "n.68T>C",
"hgvs_p": null,
"transcript": "ENST00000559265.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SELENON",
"gene_hgnc_id": 15999,
"dbsnp": "rs973033318",
"frequency_reference_population": 0.000013143368,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.0000131434,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8421087265014648,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.42399999499320984,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.855,
"revel_prediction": "Pathogenic",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.991,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.06,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.428076851998431,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000361547.7",
"gene_symbol": "SELENON",
"hgnc_id": 15999,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1094T>C",
"hgvs_p": "p.Met365Thr"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000559265.1",
"gene_symbol": "ENSG00000255054",
"hgnc_id": null,
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.68T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Eichsfeld type congenital muscular dystrophy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Eichsfeld type congenital muscular dystrophy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}