rs558031489
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_201384.3(PLEC):c.2736C>T(p.Ala912=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,609,964 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. A912A) has been classified as Likely benign.
Frequency
Consequence
NM_201384.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEC | NM_201384.3 | c.2736C>T | p.Ala912= | synonymous_variant | 22/32 | ENST00000345136.8 | |
PLEC | NM_201378.4 | c.2694C>T | p.Ala898= | synonymous_variant | 22/32 | ENST00000356346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.2736C>T | p.Ala912= | synonymous_variant | 22/32 | 1 | NM_201384.3 | ||
PLEC | ENST00000356346.7 | c.2694C>T | p.Ala898= | synonymous_variant | 22/32 | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000415 AC: 10AN: 240722Hom.: 0 AF XY: 0.0000454 AC XY: 6AN XY: 132220
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1457808Hom.: 0 Cov.: 65 AF XY: 0.0000441 AC XY: 32AN XY: 725348
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
Epidermolysis bullosa simplex, Ogna type;C2677349:Epidermolysis bullosa simplex 5C, with pyloric atresia;C2931072:Epidermolysis bullosa simplex 5B, with muscular dystrophy;C3150989:Autosomal recessive limb-girdle muscular dystrophy type 2Q;C4225309:Epidermolysis bullosa simplex with nail dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 31, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at