11-66599214-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005125.2(CCS):c.211C>T(p.Arg71Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,612,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005125.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152004Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249350Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134812
GnomAD4 exome AF: 0.000108 AC: 158AN: 1460536Hom.: 0 Cov.: 31 AF XY: 0.0000963 AC XY: 70AN XY: 726590
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152004Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.211C>T (p.R71W) alteration is located in exon 3 (coding exon 3) of the CCS gene. This alteration results from a C to T substitution at nucleotide position 211, causing the arginine (R) at amino acid position 71 to be replaced by a tryptophan (W). 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