5-80654731-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002439.5(MSH3):c.4T>A(p.Ser2Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S2F) has been classified as Uncertain significance.
Frequency
Consequence
NM_002439.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSH3 | NM_002439.5 | c.4T>A | p.Ser2Thr | missense_variant | 1/24 | ENST00000265081.7 | |
DHFR | NM_000791.4 | c.-242A>T | 5_prime_UTR_variant | 1/6 | ENST00000439211.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSH3 | ENST00000265081.7 | c.4T>A | p.Ser2Thr | missense_variant | 1/24 | 1 | NM_002439.5 | P2 | |
DHFR | ENST00000439211.7 | c.-242A>T | 5_prime_UTR_variant | 1/6 | 1 | NM_000791.4 | P1 | ||
MSH3 | ENST00000667069.1 | c.4T>A | p.Ser2Thr | missense_variant | 1/22 | ||||
MSH3 | ENST00000670357.1 | c.4T>A | p.Ser2Thr | missense_variant, NMD_transcript_variant | 1/25 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 35
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Endometrial carcinoma Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Sep 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.