rs369344419
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_201384.3(PLEC):c.2477A>G(p.Asp826Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000742 in 1,603,396 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D826D) has been classified as Likely benign.
Frequency
Consequence
NM_201384.3 missense
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.2477A>G | p.Asp826Gly | missense_variant | 21/32 | ENST00000345136.8 | |
PLEC | NM_201378.4 | c.2435A>G | p.Asp812Gly | missense_variant | 21/32 | ENST00000356346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.2477A>G | p.Asp826Gly | missense_variant | 21/32 | 1 | NM_201384.3 | ||
PLEC | ENST00000356346.7 | c.2435A>G | p.Asp812Gly | missense_variant | 21/32 | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152196Hom.: 2 Cov.: 34
GnomAD3 exomes AF: 0.000156 AC: 36AN: 230206Hom.: 0 AF XY: 0.000134 AC XY: 17AN XY: 126894
GnomAD4 exome AF: 0.0000648 AC: 94AN: 1451082Hom.: 1 Cov.: 65 AF XY: 0.0000471 AC XY: 34AN XY: 721996
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152314Hom.: 2 Cov.: 34 AF XY: 0.0000806 AC XY: 6AN XY: 74480
ClinVar
Submissions by phenotype
not provided Uncertain:3Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 19, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 11, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 30, 2018 | This variant is associated with the following publications: (PMID: 31269534) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Nov 29, 2022 | PP3, PM2 - |
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 | Nov 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at