rs201818691
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_201384.3(PLEC):c.2458-8C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00207 in 1,599,848 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_201384.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEC | NM_201378.4 | c.2416-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000356346.7 | |||
PLEC | NM_201384.3 | c.2458-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000345136.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.2458-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_201384.3 | ||||
PLEC | ENST00000356346.7 | c.2416-8C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00154 AC: 235AN: 152206Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00124 AC: 275AN: 222644Hom.: 1 AF XY: 0.00130 AC XY: 159AN XY: 122670
GnomAD4 exome AF: 0.00213 AC: 3080AN: 1447524Hom.: 5 Cov.: 65 AF XY: 0.00209 AC XY: 1507AN XY: 719862
GnomAD4 genome ? AF: 0.00154 AC: 235AN: 152324Hom.: 0 Cov.: 34 AF XY: 0.00149 AC XY: 111AN XY: 74490
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 16, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 29, 2015 | - - |
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 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at