17-17522388-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_148172.3(PEMT):c.212G>A(p.Arg71Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000112 in 1,610,638 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_148172.3 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: 0.0000132 AC: 2AN: 151376Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 250310Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135560
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1459262Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 726152
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151376Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73882
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.101G>A (p.R34Q) alteration is located in exon 3 (coding exon 2) of the PEMT gene. This alteration results from a G to A substitution at nucleotide position 101, causing the arginine (R) at amino acid position 34 to be replaced by a glutamine (Q). 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