chr1-15725495-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015164.4(PLEKHM2):āc.891G>Cā(p.Glu297Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00423 in 1,580,838 control chromosomes in the GnomAD database, including 29 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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. E297A) 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHM2 | NM_015164.4 | c.891G>C | p.Glu297Asp | missense_variant | 8/20 | ENST00000375799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHM2 | ENST00000375799.8 | c.891G>C | p.Glu297Asp | missense_variant | 8/20 | 1 | NM_015164.4 | P2 | |
ENST00000453804.1 | n.212-2208C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00342 AC: 520AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00413 AC: 812AN: 196436Hom.: 3 AF XY: 0.00417 AC XY: 442AN XY: 105926
GnomAD4 exome AF: 0.00432 AC: 6171AN: 1428472Hom.: 29 Cov.: 31 AF XY: 0.00439 AC XY: 3105AN XY: 707396
GnomAD4 genome AF: 0.00341 AC: 519AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.00315 AC XY: 235AN XY: 74508
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