chr8-143924702-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_201384.3(PLEC):c.5227G>A(p.Ala1743Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000456 in 1,534,416 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A1743V) has been classified as Uncertain significance.
Frequency
Consequence
NM_201384.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEC | NM_201384.3 | c.5227G>A | p.Ala1743Thr | missense_variant | 31/32 | ENST00000345136.8 | |
PLEC | NM_201378.4 | c.5185G>A | p.Ala1729Thr | missense_variant | 31/32 | ENST00000356346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.5227G>A | p.Ala1743Thr | missense_variant | 31/32 | 1 | NM_201384.3 | ||
PLEC | ENST00000356346.7 | c.5185G>A | p.Ala1729Thr | missense_variant | 31/32 | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes AF: 0.000460 AC: 70AN: 152048Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.000489 AC: 63AN: 128842Hom.: 0 AF XY: 0.000468 AC XY: 33AN XY: 70544
GnomAD4 exome AF: 0.000456 AC: 630AN: 1382368Hom.: 1 Cov.: 68 AF XY: 0.000504 AC XY: 344AN XY: 682188
GnomAD4 genome AF: 0.000460 AC: 70AN: 152048Hom.: 0 Cov.: 35 AF XY: 0.000458 AC XY: 34AN XY: 74252
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 21, 2019 | This variant is associated with the following publications: (PMID: 31862442) - |
Likely benign, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 27, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 26, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 23, 2015 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2018 | - - |
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 | Dec 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at