3-14145808-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_004628.5(XPC):c.*133G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,145,242 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004628.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000545 AC: 83AN: 152170Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00224 AC: 346AN: 154570Hom.: 3 AF XY: 0.00294 AC XY: 244AN XY: 83032
GnomAD4 exome AF: 0.00107 AC: 1063AN: 992954Hom.: 16 Cov.: 13 AF XY: 0.00154 AC XY: 781AN XY: 505844
GnomAD4 genome AF: 0.000538 AC: 82AN: 152288Hom.: 1 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74450
ClinVar
Submissions by phenotype
Xeroderma pigmentosum Uncertain:1
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Arrhythmogenic right ventricular cardiomyopathy Benign:1
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Xeroderma pigmentosum, group C Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at