X-91877792-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_032968.5(PCDH11X):c.1552C>T(p.Arg518Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000237 in 1,098,021 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032968.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183195Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67783
GnomAD4 exome AF: 0.0000237 AC: 26AN: 1098021Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 7AN XY: 363497
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1552C>T (p.R518C) alteration is located in exon 2 (coding exon 2) of the PCDH11X gene. This alteration results from a C to T substitution at nucleotide position 1552, causing the arginine (R) at amino acid position 518 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