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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: 12-56752285-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=56752285&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 56752285,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000338193.11",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "c.14A>C",
"hgvs_p": "p.Asp5Ala",
"transcript": "NM_000946.3",
"protein_id": "NP_000937.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 420,
"cds_start": 14,
"cds_end": null,
"cds_length": 1263,
"cdna_start": 39,
"cdna_end": null,
"cdna_length": 1423,
"mane_select": "ENST00000338193.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "c.14A>C",
"hgvs_p": "p.Asp5Ala",
"transcript": "ENST00000338193.11",
"protein_id": "ENSP00000350491.5",
"transcript_support_level": 1,
"aa_start": 5,
"aa_end": null,
"aa_length": 420,
"cds_start": 14,
"cds_end": null,
"cds_length": 1263,
"cdna_start": 39,
"cdna_end": null,
"cdna_length": 1423,
"mane_select": "NM_000946.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "c.14A>C",
"hgvs_p": "p.Asp5Ala",
"transcript": "ENST00000672280.1",
"protein_id": "ENSP00000500157.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 459,
"cds_start": 14,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 90,
"cdna_end": null,
"cdna_length": 1875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "c.14A>C",
"hgvs_p": "p.Asp5Ala",
"transcript": "ENST00000706567.1",
"protein_id": "ENSP00000516452.1",
"transcript_support_level": null,
"aa_start": 5,
"aa_end": null,
"aa_length": 425,
"cds_start": 14,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 90,
"cdna_end": null,
"cdna_length": 1684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "c.14A>C",
"hgvs_p": "p.Asp5Ala",
"transcript": "ENST00000550770.1",
"protein_id": "ENSP00000450185.1",
"transcript_support_level": 5,
"aa_start": 5,
"aa_end": null,
"aa_length": 326,
"cds_start": 14,
"cds_end": null,
"cds_length": 983,
"cdna_start": 39,
"cdna_end": null,
"cdna_length": 1008,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "n.55A>C",
"hgvs_p": null,
"transcript": "ENST00000548173.5",
"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": 590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "n.29A>C",
"hgvs_p": null,
"transcript": "ENST00000550224.5",
"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": 1206,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "n.14A>C",
"hgvs_p": null,
"transcript": "ENST00000552590.6",
"protein_id": "ENSP00000448178.1",
"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": 1459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "n.14A>C",
"hgvs_p": null,
"transcript": "ENST00000706566.1",
"protein_id": "ENSP00000516451.1",
"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": 1726,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B6",
"gene_hgnc_id": 23316,
"hgvs_c": "c.-53T>G",
"hgvs_p": null,
"transcript": "ENST00000555159.5",
"protein_id": "ENSP00000450698.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B6",
"gene_hgnc_id": 23316,
"hgvs_c": "c.-250T>G",
"hgvs_p": null,
"transcript": "ENST00000555805.5",
"protein_id": "ENSP00000451753.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1722,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B6",
"gene_hgnc_id": 23316,
"hgvs_c": "c.-527T>G",
"hgvs_p": null,
"transcript": "ENST00000554150.5",
"protein_id": "ENSP00000452273.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B6",
"gene_hgnc_id": 23316,
"hgvs_c": "c.-513T>G",
"hgvs_p": null,
"transcript": "ENST00000554643.5",
"protein_id": "ENSP00000451406.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 317,
"cds_start": -4,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B6",
"gene_hgnc_id": 23316,
"hgvs_c": "c.-528T>G",
"hgvs_p": null,
"transcript": "ENST00000554155.1",
"protein_id": "ENSP00000451497.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 87,
"cds_start": -4,
"cds_end": null,
"cds_length": 266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B6",
"gene_hgnc_id": 23316,
"hgvs_c": "c.-533T>G",
"hgvs_p": null,
"transcript": "ENST00000556650.5",
"protein_id": "ENSP00000452103.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 74,
"cds_start": -4,
"cds_end": null,
"cds_length": 226,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 591,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"hgvs_c": "n.-16A>C",
"hgvs_p": null,
"transcript": "ENST00000546761.5",
"protein_id": null,
"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": 381,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HSD17B6",
"gene_hgnc_id": 23316,
"hgvs_c": "n.-172T>G",
"hgvs_p": null,
"transcript": "ENST00000556481.5",
"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": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRIM1",
"gene_hgnc_id": 9369,
"dbsnp": "rs2277339",
"frequency_reference_population": 0.11455339,
"hom_count_reference_population": 11085,
"allele_count_reference_population": 180916,
"gnomad_exomes_af": 0.111924,
"gnomad_genomes_af": 0.139732,
"gnomad_exomes_ac": 160047,
"gnomad_genomes_ac": 20869,
"gnomad_exomes_homalt": 9501,
"gnomad_genomes_homalt": 1584,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.001611083745956421,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.233,
"revel_prediction": "Benign",
"alphamissense_score": 0.1693,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.25,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.994,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000338193.11",
"gene_symbol": "PRIM1",
"hgnc_id": 9369,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.14A>C",
"hgvs_p": "p.Asp5Ala"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000555159.5",
"gene_symbol": "HSD17B6",
"hgnc_id": 23316,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-53T>G",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}