rs61738983
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015164.4(PLEKHM2):āc.1084C>Gā(p.Arg362Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 1,597,150 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R362L) has been classified as Uncertain significance.
Frequency
Consequence
NM_015164.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHM2 | NM_015164.4 | c.1084C>G | p.Arg362Gly | missense_variant | 9/20 | ENST00000375799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHM2 | ENST00000375799.8 | c.1084C>G | p.Arg362Gly | missense_variant | 9/20 | 1 | NM_015164.4 | P2 | |
ENST00000453804.1 | n.212-3869G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00712 AC: 1083AN: 152112Hom.: 13 Cov.: 32
GnomAD3 exomes AF: 0.00162 AC: 370AN: 228468Hom.: 5 AF XY: 0.00111 AC XY: 139AN XY: 125130
GnomAD4 exome AF: 0.000714 AC: 1032AN: 1444920Hom.: 15 Cov.: 33 AF XY: 0.000618 AC XY: 443AN XY: 716532
GnomAD4 genome ? AF: 0.00711 AC: 1083AN: 152230Hom.: 13 Cov.: 32 AF XY: 0.00676 AC XY: 503AN XY: 74432
ClinVar
Submissions by phenotype
Dilated Cardiomyopathy, Recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at