1-12861477-T-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000240189.2(PRAMEF2):āc.1123T>Cā(p.Cys375Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 1,505,846 control chromosomes in the GnomAD database, including 56,208 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000240189.2 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 |
---|---|---|---|---|---|---|---|---|
PRAMEF2 | NM_023014.1 | c.1123T>C | p.Cys375Arg | missense_variant | 4/4 | ENST00000240189.2 | NP_075390.1 | |
PRAMEF2 | XM_011542004.1 | c.388T>C | p.Cys130Arg | missense_variant | 2/2 | XP_011540306.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRAMEF2 | ENST00000240189.2 | c.1123T>C | p.Cys375Arg | missense_variant | 4/4 | 1 | NM_023014.1 | ENSP00000240189 | P1 |
Frequencies
GnomAD3 genomes AF: 0.288 AC: 39689AN: 137696Hom.: 6676 Cov.: 30
GnomAD4 exome AF: 0.247 AC: 338303AN: 1368044Hom.: 49514 Cov.: 61 AF XY: 0.246 AC XY: 167212AN XY: 680852
GnomAD4 genome AF: 0.288 AC: 39736AN: 137802Hom.: 6694 Cov.: 30 AF XY: 0.288 AC XY: 19381AN XY: 67182
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
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