rs200751865
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_201384.3(PLEC):c.5696G>T(p.Arg1899Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,968 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1899C) has been classified as Uncertain significance.
Frequency
Consequence
NM_201384.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEC | NM_201384.3 | c.5696G>T | p.Arg1899Leu | missense_variant | 31/32 | ENST00000345136.8 | |
PLEC | NM_201378.4 | c.5654G>T | p.Arg1885Leu | missense_variant | 31/32 | ENST00000356346.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEC | ENST00000345136.8 | c.5696G>T | p.Arg1899Leu | missense_variant | 31/32 | 1 | NM_201384.3 | ||
PLEC | ENST00000356346.7 | c.5654G>T | p.Arg1885Leu | missense_variant | 31/32 | 1 | NM_201378.4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151968Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.00000437 AC: 1AN: 228936Hom.: 0 AF XY: 0.00000790 AC XY: 1AN XY: 126526
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1446386Hom.: 0 Cov.: 73 AF XY: 0.00 AC XY: 0AN XY: 720138
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151968Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74218
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at