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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: 8-47778507-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=47778507&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 47778507,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_006904.7",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 83,
"exon_rank_end": null,
"exon_count": 86,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.11805C>T",
"hgvs_p": "p.Gly3935Gly",
"transcript": "NM_006904.7",
"protein_id": "NP_008835.5",
"transcript_support_level": null,
"aa_start": 3935,
"aa_end": null,
"aa_length": 4128,
"cds_start": 11805,
"cds_end": null,
"cds_length": 12387,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000314191.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006904.7"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 83,
"exon_rank_end": null,
"exon_count": 86,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.11805C>T",
"hgvs_p": "p.Gly3935Gly",
"transcript": "ENST00000314191.7",
"protein_id": "ENSP00000313420.3",
"transcript_support_level": 1,
"aa_start": 3935,
"aa_end": null,
"aa_length": 4128,
"cds_start": 11805,
"cds_end": null,
"cds_length": 12387,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006904.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000314191.7"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 85,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.11712C>T",
"hgvs_p": "p.Gly3904Gly",
"transcript": "ENST00000338368.7",
"protein_id": "ENSP00000345182.4",
"transcript_support_level": 1,
"aa_start": 3904,
"aa_end": null,
"aa_length": 4097,
"cds_start": 11712,
"cds_end": null,
"cds_length": 12294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000338368.7"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 83,
"exon_rank_end": null,
"exon_count": 86,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.11814C>T",
"hgvs_p": "p.Gly3938Gly",
"transcript": "ENST00000911724.1",
"protein_id": "ENSP00000581783.1",
"transcript_support_level": null,
"aa_start": 3938,
"aa_end": null,
"aa_length": 4131,
"cds_start": 11814,
"cds_end": null,
"cds_length": 12396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911724.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 83,
"exon_rank_end": null,
"exon_count": 86,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.11808C>T",
"hgvs_p": "p.Gly3936Gly",
"transcript": "ENST00000911723.1",
"protein_id": "ENSP00000581782.1",
"transcript_support_level": null,
"aa_start": 3936,
"aa_end": null,
"aa_length": 4129,
"cds_start": 11808,
"cds_end": null,
"cds_length": 12390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911723.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 82,
"exon_rank_end": null,
"exon_count": 85,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.11712C>T",
"hgvs_p": "p.Gly3904Gly",
"transcript": "NM_001081640.2",
"protein_id": "NP_001075109.1",
"transcript_support_level": null,
"aa_start": 3904,
"aa_end": null,
"aa_length": 4097,
"cds_start": 11712,
"cds_end": null,
"cds_length": 12294,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001081640.2"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.4482C>T",
"hgvs_p": "p.Gly1494Gly",
"transcript": "ENST00000697603.1",
"protein_id": "ENSP00000513358.1",
"transcript_support_level": null,
"aa_start": 1494,
"aa_end": null,
"aa_length": 1687,
"cds_start": 4482,
"cds_end": null,
"cds_length": 5064,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000697603.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "c.30C>T",
"hgvs_p": "p.Gly10Gly",
"transcript": "ENST00000536429.1",
"protein_id": "ENSP00000442177.1",
"transcript_support_level": 3,
"aa_start": 10,
"aa_end": null,
"aa_length": 89,
"cds_start": 30,
"cds_end": null,
"cds_length": 270,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000536429.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.1039C>T",
"hgvs_p": null,
"transcript": "ENST00000521331.5",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000521331.5"
},
{
"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": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.213C>T",
"hgvs_p": null,
"transcript": "ENST00000536483.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000536483.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.1076C>T",
"hgvs_p": null,
"transcript": "ENST00000697601.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000697601.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.2378C>T",
"hgvs_p": null,
"transcript": "ENST00000697602.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000697602.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.1113C>T",
"hgvs_p": null,
"transcript": "ENST00000697604.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000697604.1"
},
{
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.1072C>T",
"hgvs_p": null,
"transcript": "ENST00000697605.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000697605.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"hgvs_c": "n.*30C>T",
"hgvs_p": null,
"transcript": "ENST00000536710.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "retained_intron",
"feature": "ENST00000536710.1"
}
],
"gene_symbol": "PRKDC",
"gene_hgnc_id": 9413,
"dbsnp": "rs8178249",
"frequency_reference_population": 0.005365742,
"hom_count_reference_population": 57,
"allele_count_reference_population": 8658,
"gnomad_exomes_af": 0.00534127,
"gnomad_genomes_af": 0.00560049,
"gnomad_exomes_ac": 7805,
"gnomad_genomes_ac": 853,
"gnomad_exomes_homalt": 49,
"gnomad_genomes_homalt": 8,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004999999888241291,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.005,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.333,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_006904.7",
"gene_symbol": "PRKDC",
"hgnc_id": 9413,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.11805C>T",
"hgvs_p": "p.Gly3935Gly"
}
],
"clinvar_disease": "Severe combined immunodeficiency due to DNA-PKcs deficiency,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4 B:1",
"phenotype_combined": "not specified|Severe combined immunodeficiency due to DNA-PKcs deficiency|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}