2-44332628-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_001171613.2(PREPL):āc.917T>Cā(p.Met306Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,613,880 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001171613.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREPL | NM_001171613.2 | c.917T>C | p.Met306Thr | missense_variant | 8/14 | ENST00000409411.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREPL | ENST00000409411.6 | c.917T>C | p.Met306Thr | missense_variant | 8/14 | 1 | NM_001171613.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000618 AC: 94AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251090Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135718
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461540Hom.: 1 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727090
GnomAD4 genome AF: 0.000617 AC: 94AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000644 AC XY: 48AN XY: 74490
ClinVar
Submissions by phenotype
Myasthenic syndrome, congenital, 22 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at