rs181186746
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015164.4(PLEKHM2):āc.2329A>Gā(p.Met777Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000364 in 1,610,420 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_015164.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHM2 | NM_015164.4 | c.2329A>G | p.Met777Val | missense_variant | 15/20 | ENST00000375799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHM2 | ENST00000375799.8 | c.2329A>G | p.Met777Val | missense_variant | 15/20 | 1 | NM_015164.4 | P2 | |
ENST00000453804.1 | n.211+1735T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00197 AC: 300AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000446 AC: 108AN: 241892Hom.: 0 AF XY: 0.000365 AC XY: 48AN XY: 131534
GnomAD4 exome AF: 0.000196 AC: 286AN: 1458134Hom.: 1 Cov.: 32 AF XY: 0.000167 AC XY: 121AN XY: 724982
GnomAD4 genome ? AF: 0.00197 AC: 300AN: 152286Hom.: 0 Cov.: 33 AF XY: 0.00183 AC XY: 136AN XY: 74470
ClinVar
Submissions by phenotype
Dilated Cardiomyopathy, Recessive Benign:1
Likely 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