rs200062782
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_201384.3(PLEC):c.6426C>T(p.Ala2142Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,597,858 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).
Frequency
Consequence
NM_201384.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.6426C>T | p.Ala2142Ala | synonymous_variant | Exon 31 of 32 | 1 | NM_201384.3 | ENSP00000344848.3 | ||
PLEC | ENST00000356346.7 | c.6384C>T | p.Ala2128Ala | synonymous_variant | Exon 31 of 32 | 1 | NM_201378.4 | ENSP00000348702.3 |
Frequencies
GnomAD3 genomes AF: 0.000568 AC: 86AN: 151412Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000635 AC: 144AN: 226914Hom.: 0 AF XY: 0.000651 AC XY: 82AN XY: 126012
GnomAD4 exome AF: 0.000493 AC: 713AN: 1446330Hom.: 3 Cov.: 83 AF XY: 0.000502 AC XY: 361AN XY: 719796
GnomAD4 genome AF: 0.000568 AC: 86AN: 151528Hom.: 0 Cov.: 34 AF XY: 0.000675 AC XY: 50AN XY: 74030
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:4
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PLEC: BP4, BP7 -
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not specified Benign:1
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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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at