rs753956705
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015164.4(PLEKHM2):c.909G>A(p.Pro303=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000489 in 1,574,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P303P) has been classified as Likely benign.
Frequency
Consequence
NM_015164.4 synonymous
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.909G>A | p.Pro303= | synonymous_variant | 8/20 | ENST00000375799.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHM2 | ENST00000375799.8 | c.909G>A | p.Pro303= | synonymous_variant | 8/20 | 1 | NM_015164.4 | P2 | |
ENST00000453804.1 | n.212-2226C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000646 AC: 12AN: 185654Hom.: 0 AF XY: 0.0000401 AC XY: 4AN XY: 99708
GnomAD4 exome AF: 0.0000429 AC: 61AN: 1422374Hom.: 0 Cov.: 31 AF XY: 0.0000398 AC XY: 28AN XY: 703748
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74502
ClinVar
Submissions by phenotype
Dilated Cardiomyopathy, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at