19-15052249-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_012114.3(CASP14):c.-3G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000241 in 1,591,444 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_012114.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152182Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000405 AC: 9AN: 222444Hom.: 0 AF XY: 0.0000500 AC XY: 6AN XY: 120080
GnomAD4 exome AF: 0.000261 AC: 376AN: 1439262Hom.: 0 Cov.: 30 AF XY: 0.000253 AC XY: 181AN XY: 714732
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
CASP14-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at