19-55092637-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017607.4(PPP1R12C):c.1937G>T(p.Arg646Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000848 in 1,533,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. R646G) has been classified as Uncertain significance.
Frequency
Consequence
NM_017607.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152074Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000417 AC: 6AN: 144030Hom.: 0 AF XY: 0.0000388 AC XY: 3AN XY: 77394
GnomAD4 exome AF: 0.00000724 AC: 10AN: 1381498Hom.: 0 Cov.: 44 AF XY: 0.00000735 AC XY: 5AN XY: 680144
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152192Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74426
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1937G>T (p.R646L) alteration is located in exon 17 (coding exon 17) of the PPP1R12C gene. This alteration results from a G to T substitution at nucleotide position 1937, causing the arginine (R) at amino acid position 646 to be replaced by a leucine (L). 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