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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: 6-30562080-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=30562080&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 30562080,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_025263.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "c.416T>C",
"hgvs_p": "p.Ile139Thr",
"transcript": "NM_025263.4",
"protein_id": "NP_079539.2",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 188,
"cds_start": 416,
"cds_end": null,
"cds_length": 567,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 1845,
"mane_select": "ENST00000376560.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_025263.4"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "c.416T>C",
"hgvs_p": "p.Ile139Thr",
"transcript": "ENST00000376560.8",
"protein_id": "ENSP00000365744.4",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 188,
"cds_start": 416,
"cds_end": null,
"cds_length": 567,
"cdna_start": 466,
"cdna_end": null,
"cdna_length": 1845,
"mane_select": "NM_025263.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376560.8"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "c.353T>C",
"hgvs_p": "p.Ile118Thr",
"transcript": "NM_001077497.3",
"protein_id": "NP_001070965.1",
"transcript_support_level": null,
"aa_start": 118,
"aa_end": null,
"aa_length": 167,
"cds_start": 353,
"cds_end": null,
"cds_length": 504,
"cdna_start": 989,
"cdna_end": null,
"cdna_length": 2368,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001077497.3"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "c.353T>C",
"hgvs_p": "p.Ile118Thr",
"transcript": "ENST00000376557.3",
"protein_id": "ENSP00000365740.3",
"transcript_support_level": 2,
"aa_start": 118,
"aa_end": null,
"aa_length": 167,
"cds_start": 353,
"cds_end": null,
"cds_length": 504,
"cdna_start": 418,
"cdna_end": null,
"cdna_length": 1797,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376557.3"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "c.107-309T>C",
"hgvs_p": null,
"transcript": "ENST00000934408.1",
"protein_id": "ENSP00000604467.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 70,
"cds_start": null,
"cds_end": null,
"cds_length": 213,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1512,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934408.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "n.2050T>C",
"hgvs_p": null,
"transcript": "ENST00000470703.1",
"protein_id": null,
"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": 3429,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000470703.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "n.565T>C",
"hgvs_p": null,
"transcript": "ENST00000481741.5",
"protein_id": null,
"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": 1944,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000481741.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"hgvs_c": "n.626T>C",
"hgvs_p": null,
"transcript": "ENST00000498336.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 2005,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000498336.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290047",
"gene_hgnc_id": null,
"hgvs_c": "n.188-3421A>G",
"hgvs_p": null,
"transcript": "ENST00000832105.1",
"protein_id": null,
"transcript_support_level": null,
"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": 756,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000832105.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000290047",
"gene_hgnc_id": null,
"hgvs_c": "n.253+1692A>G",
"hgvs_p": null,
"transcript": "ENST00000832106.1",
"protein_id": null,
"transcript_support_level": null,
"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": 820,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000832106.1"
}
],
"gene_symbol": "PRR3",
"gene_hgnc_id": 21149,
"dbsnp": "rs753276760",
"frequency_reference_population": 6.863352e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.86335e-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": 0.05844491720199585,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.076,
"revel_prediction": "Benign",
"alphamissense_score": 0.4444,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.352,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_025263.4",
"gene_symbol": "PRR3",
"hgnc_id": 21149,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.416T>C",
"hgvs_p": "p.Ile139Thr"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000832105.1",
"gene_symbol": "ENSG00000290047",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.188-3421A>G",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}