rs782073897
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_201384.3(PLEC):c.4758C>T(p.Ala1586=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000166 in 1,563,344 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. A1586A) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEC | NM_201384.3 | c.4758C>T | p.Ala1586= | synonymous_variant | 31/32 | ENST00000345136.8 | |
PLEC | NM_201378.4 | c.4716C>T | p.Ala1572= | synonymous_variant | 31/32 | ENST00000356346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.4758C>T | p.Ala1586= | synonymous_variant | 31/32 | 1 | NM_201384.3 | ||
PLEC | ENST00000356346.7 | c.4716C>T | p.Ala1572= | synonymous_variant | 31/32 | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152006Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000237 AC: 4AN: 168442Hom.: 0 AF XY: 0.0000322 AC XY: 3AN XY: 93186
GnomAD4 exome AF: 0.0000156 AC: 22AN: 1411338Hom.: 0 Cov.: 68 AF XY: 0.0000214 AC XY: 15AN XY: 699580
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152006Hom.: 0 Cov.: 35 AF XY: 0.0000404 AC XY: 3AN XY: 74250
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 02, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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 | Oct 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at