chr11-396865-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007183.4(PKP3):c.364C>T(p.Arg122Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000485 in 1,600,020 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R122H) has been classified as Uncertain significance.
Frequency
Consequence
NM_007183.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00231 AC: 351AN: 152222Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.000721 AC: 159AN: 220474Hom.: 0 AF XY: 0.000567 AC XY: 69AN XY: 121652
GnomAD4 exome AF: 0.000294 AC: 425AN: 1447680Hom.: 2 Cov.: 34 AF XY: 0.000265 AC XY: 191AN XY: 719830
GnomAD4 genome AF: 0.00230 AC: 351AN: 152340Hom.: 1 Cov.: 34 AF XY: 0.00238 AC XY: 177AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at