← Back to variant description
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: 12-47879112-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=47879112&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 47879112,
"ref": "A",
"alt": "G",
"effect": "start_lost",
"transcript": "NM_001364085.2",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_000376.3",
"protein_id": "NP_000367.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 427,
"cds_start": 2,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000549336.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000376.3"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000549336.6",
"protein_id": "ENSP00000449573.2",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 427,
"cds_start": 2,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000376.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549336.6"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.152T>C",
"hgvs_p": "p.Met51Thr",
"transcript": "ENST00000550325.5",
"protein_id": "ENSP00000447173.1",
"transcript_support_level": 1,
"aa_start": 51,
"aa_end": null,
"aa_length": 477,
"cds_start": 152,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000550325.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001364085.2",
"protein_id": "NP_001351014.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 494,
"cds_start": 2,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001364085.2"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000229022.9",
"protein_id": "ENSP00000229022.5",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 494,
"cds_start": 2,
"cds_end": null,
"cds_length": 1485,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000229022.9"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001017535.2",
"protein_id": "NP_001017535.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 427,
"cds_start": 2,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001017535.2"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001374661.1",
"protein_id": "NP_001361590.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 427,
"cds_start": 2,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374661.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "NM_001374662.1",
"protein_id": "NP_001361591.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 427,
"cds_start": 2,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001374662.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000395324.6",
"protein_id": "ENSP00000378734.2",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 427,
"cds_start": 2,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395324.6"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000546653.5",
"protein_id": "ENSP00000448659.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 249,
"cds_start": 2,
"cds_end": null,
"cds_length": 751,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000546653.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000891950.1",
"protein_id": "ENSP00000562009.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 224,
"cds_start": 2,
"cds_end": null,
"cds_length": 675,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000891950.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000550314.5",
"protein_id": "ENSP00000449561.1",
"transcript_support_level": 3,
"aa_start": 1,
"aa_end": null,
"aa_length": 105,
"cds_start": 2,
"cds_end": null,
"cds_length": 318,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000550314.5"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000548664.1",
"protein_id": "ENSP00000450105.1",
"transcript_support_level": 5,
"aa_start": 1,
"aa_end": null,
"aa_length": 100,
"cds_start": 2,
"cds_end": null,
"cds_length": 305,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548664.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?",
"transcript": "XM_047429500.1",
"protein_id": "XP_047285456.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 427,
"cds_start": 2,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047429500.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.152T>C",
"hgvs_p": "p.Met51Thr",
"transcript": "NM_001017536.2",
"protein_id": "NP_001017536.1",
"transcript_support_level": null,
"aa_start": 51,
"aa_end": null,
"aa_length": 477,
"cds_start": 152,
"cds_end": null,
"cds_length": 1434,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001017536.2"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "c.71T>C",
"hgvs_p": "p.Met24Thr",
"transcript": "XM_024449178.2",
"protein_id": "XP_024304946.1",
"transcript_support_level": null,
"aa_start": 24,
"aa_end": null,
"aa_length": 450,
"cds_start": 71,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024449178.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"hgvs_c": "n.2T>C",
"hgvs_p": null,
"transcript": "ENST00000547065.1",
"protein_id": "ENSP00000449074.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000547065.1"
}
],
"gene_symbol": "VDR",
"gene_hgnc_id": 12679,
"dbsnp": "rs2228570",
"frequency_reference_population": 0.628776,
"hom_count_reference_population": 321917,
"allele_count_reference_population": 1014510,
"gnomad_exomes_af": 0.62531,
"gnomad_genomes_af": 0.662142,
"gnomad_exomes_ac": 913981,
"gnomad_genomes_ac": 100529,
"gnomad_exomes_homalt": 288010,
"gnomad_genomes_homalt": 33907,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.000008306144991365727,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.503,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.2321,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.354,
"phylop100way_prediction": "Uncertain_significance",
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "PVS1_Supporting,BP6,BA1",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 9,
"pathogenic_score": 1,
"criteria": [
"PVS1_Supporting",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001364085.2",
"gene_symbol": "VDR",
"hgnc_id": 12679,
"effects": [
"start_lost"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2T>C",
"hgvs_p": "p.Met1?"
}
],
"clinvar_disease": "Periodontitis,Vitamin D-dependent rickets type II with alopecia,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 B:8",
"phenotype_combined": "Vitamin D-dependent rickets type II with alopecia|not provided|Periodontitis|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}