7-143573090-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001008747.2(CTAGE15):c.1273C>T(p.Arg425Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 11/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R425L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001008747.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000323 AC: 4AN: 123694Hom.: 1 Cov.: 17
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000125 AC: 16AN: 1285036Hom.: 2 Cov.: 33 AF XY: 0.0000125 AC XY: 8AN XY: 639336
GnomAD4 genome AF: 0.0000323 AC: 4AN: 123694Hom.: 1 Cov.: 17 AF XY: 0.0000167 AC XY: 1AN XY: 59738
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1273C>T (p.R425C) alteration is located in exon 1 (coding exon 1) of the CTAGE15 gene. This alteration results from a C to T substitution at nucleotide position 1273, causing the arginine (R) at amino acid position 425 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at