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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: 2-158176652-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=158176652&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CCDC148",
"hgnc_id": 25191,
"hgvs_c": "c.1498G>T",
"hgvs_p": "p.Val500Phe",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_138803.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "CCDC148-AS1",
"hgnc_id": 44134,
"hgvs_c": "n.126C>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000412781.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 2,
"alphamissense_prediction": null,
"alphamissense_score": 0.1432,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.35,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.6958584785461426,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 591,
"aa_ref": "V",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 1812,
"cds_end": null,
"cds_length": 1776,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_138803.4",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "c.1498G>T",
"hgvs_p": "p.Val500Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000283233.10",
"protein_coding": true,
"protein_id": "NP_620158.3",
"strand": false,
"transcript": "NM_138803.4",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 591,
"aa_ref": "V",
"aa_start": 500,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 1812,
"cds_end": null,
"cds_length": 1776,
"cds_start": 1498,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000283233.10",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "c.1498G>T",
"hgvs_p": "p.Val500Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138803.4",
"protein_coding": true,
"protein_id": "ENSP00000283233.5",
"strand": false,
"transcript": "ENST00000283233.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 795,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000412781.2",
"gene_hgnc_id": 44134,
"gene_symbol": "CCDC148-AS1",
"hgvs_c": "n.126C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000412781.2",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1786,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000448656.5",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "n.*1089G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000415540.1",
"strand": false,
"transcript": "ENST00000448656.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1786,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000448656.5",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "n.*1089G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000415540.1",
"strand": false,
"transcript": "ENST00000448656.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 600,
"aa_ref": "V",
"aa_start": 509,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2523,
"cdna_start": 1676,
"cds_end": null,
"cds_length": 1803,
"cds_start": 1525,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000409187.5",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "c.1525G>T",
"hgvs_p": "p.Val509Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386674.1",
"strand": false,
"transcript": "ENST00000409187.5",
"transcript_support_level": 5
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 600,
"aa_ref": "V",
"aa_start": 509,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1975,
"cdna_start": 1558,
"cds_end": null,
"cds_length": 1803,
"cds_start": 1525,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000707084.1",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "c.1525G>T",
"hgvs_p": "p.Val509Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000516735.1",
"strand": false,
"transcript": "ENST00000707084.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 544,
"aa_ref": "V",
"aa_start": 453,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2861,
"cdna_start": 1645,
"cds_end": null,
"cds_length": 1635,
"cds_start": 1357,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000900274.1",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "c.1357G>T",
"hgvs_p": "p.Val453Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000570333.1",
"strand": false,
"transcript": "ENST00000900274.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 478,
"aa_ref": "V",
"aa_start": 387,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2293,
"cdna_start": 1449,
"cds_end": null,
"cds_length": 1437,
"cds_start": 1159,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000956036.1",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "c.1159G>T",
"hgvs_p": "p.Val387Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626095.1",
"strand": false,
"transcript": "ENST00000956036.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 445,
"aa_ref": "V",
"aa_start": 354,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2874,
"cdna_start": 1556,
"cds_end": null,
"cds_length": 1338,
"cds_start": 1060,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_001301684.2",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "c.1060G>T",
"hgvs_p": "p.Val354Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001288613.1",
"strand": false,
"transcript": "NM_001301684.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2075,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000454257.5",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "n.*716G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000398372.1",
"strand": false,
"transcript": "ENST00000454257.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 795,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_038850.1",
"gene_hgnc_id": 44134,
"gene_symbol": "CCDC148-AS1",
"hgvs_c": "n.126C>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_038850.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2075,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000454257.5",
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"hgvs_c": "n.*716G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000398372.1",
"strand": false,
"transcript": "ENST00000454257.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1382383371",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013703304,
"gene_hgnc_id": 25191,
"gene_symbol": "CCDC148",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000137033,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.402,
"pos": 158176652,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.101,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.11999999731779099,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.12,
"transcript": "NM_138803.4"
}
]
}