rs138555092
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001171613.2(PREPL):āc.149A>Gā(p.Asn50Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,613,670 control chromosomes in the GnomAD database, including 10 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 Benign (ā ā ).
Frequency
Consequence
NM_001171613.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PREPL | NM_001171613.2 | c.149A>G | p.Asn50Ser | missense_variant | 4/14 | ENST00000409411.6 | NP_001165084.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PREPL | ENST00000409411.6 | c.149A>G | p.Asn50Ser | missense_variant | 4/14 | 1 | NM_001171613.2 | ENSP00000387095 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00141 AC: 214AN: 152180Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00233 AC: 582AN: 250034Hom.: 2 AF XY: 0.00239 AC XY: 323AN XY: 135388
GnomAD4 exome AF: 0.00236 AC: 3443AN: 1461372Hom.: 9 Cov.: 32 AF XY: 0.00234 AC XY: 1698AN XY: 726994
GnomAD4 genome AF: 0.00141 AC: 214AN: 152298Hom.: 1 Cov.: 33 AF XY: 0.00115 AC XY: 86AN XY: 74488
ClinVar
Submissions by phenotype
Myasthenic syndrome, congenital, 22 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
PREPL-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 09, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at