rs77303974
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000345136.8(PLEC):โc.9925C>Tโ(p.Arg3309Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00758 in 1,613,096 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (โ โ ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3309H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000345136.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEC | NM_201384.3 | c.9925C>T | p.Arg3309Cys | missense_variant | 32/32 | ENST00000345136.8 | NP_958786.1 | |
PLEC | NM_201378.4 | c.9883C>T | p.Arg3295Cys | missense_variant | 32/32 | ENST00000356346.7 | NP_958780.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.9925C>T | p.Arg3309Cys | missense_variant | 32/32 | 1 | NM_201384.3 | ENSP00000344848 | ||
PLEC | ENST00000356346.7 | c.9883C>T | p.Arg3295Cys | missense_variant | 32/32 | 1 | NM_201378.4 | ENSP00000348702 |
Frequencies
GnomAD3 genomes AF: 0.00489 AC: 745AN: 152238Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00472 AC: 1171AN: 248052Hom.: 4 AF XY: 0.00459 AC XY: 620AN XY: 135000
GnomAD4 exome AF: 0.00786 AC: 11481AN: 1460742Hom.: 45 Cov.: 73 AF XY: 0.00757 AC XY: 5503AN XY: 726684
GnomAD4 genome AF: 0.00489 AC: 745AN: 152354Hom.: 4 Cov.: 33 AF XY: 0.00432 AC XY: 322AN XY: 74504
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 15, 2021 | This variant is associated with the following publications: (PMID: 29334134, 32707200) - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 26, 2018 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | PLEC: BS2 - |
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 17, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 03, 2016 | p.Arg3446Cys in exon 32 of PLEC: This variant is not expected to have clinical s ignificance because it has been identified in 0.7% (513/64856) of European chrom osomes, including two homozygotes by the Exome Aggregation Consortium (ExAC, htt p://exac.broadinstitute.org; dbSNP rs77303974). - |
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 08, 2016 | - - |
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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 25, 2024 | - - |
Autosomal recessive limb-girdle muscular dystrophy type 2Q Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Al Jalila Childrenโs Genomics Center, Al Jalila Childrens Speciality Hospital | Dec 29, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at