rs201164522
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_201384.3(PLEC):c.1629G>T(p.Glu543Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00093 in 1,612,606 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_201384.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEC | NM_201384.3 | c.1629G>T | p.Glu543Asp | missense_variant | 14/32 | ENST00000345136.8 | |
PLEC | NM_201378.4 | c.1587G>T | p.Glu529Asp | missense_variant | 14/32 | ENST00000356346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.1629G>T | p.Glu543Asp | missense_variant | 14/32 | 1 | NM_201384.3 | ||
PLEC | ENST00000356346.7 | c.1587G>T | p.Glu529Asp | missense_variant | 14/32 | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00468 AC: 712AN: 152228Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00110 AC: 269AN: 244990Hom.: 2 AF XY: 0.000747 AC XY: 100AN XY: 133782
GnomAD4 exome AF: 0.000539 AC: 787AN: 1460260Hom.: 6 Cov.: 66 AF XY: 0.000472 AC XY: 343AN XY: 726424
GnomAD4 genome ? AF: 0.00468 AC: 713AN: 152346Hom.: 6 Cov.: 33 AF XY: 0.00435 AC XY: 324AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 27, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 2017 | 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at