rs773867044
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001171613.2(PREPL):c.1520C>A(p.Thr507Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,606,470 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T507A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001171613.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREPL | NM_001171613.2 | c.1520C>A | p.Thr507Lys | missense_variant | 11/14 | ENST00000409411.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREPL | ENST00000409411.6 | c.1520C>A | p.Thr507Lys | missense_variant | 11/14 | 1 | NM_001171613.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000357 AC: 89AN: 249448Hom.: 0 AF XY: 0.000482 AC XY: 65AN XY: 134744
GnomAD4 exome AF: 0.000205 AC: 298AN: 1454282Hom.: 1 Cov.: 31 AF XY: 0.000276 AC XY: 200AN XY: 723750
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74416
ClinVar
Submissions by phenotype
Myasthenic syndrome, congenital, 22 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Genomic Research Center, Shahid Beheshti University of Medical Sciences | Jan 01, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 02, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at