2-47403090-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001258281.1(MSH2):c.-116T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000275 in 1,092,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001258281.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSH2 | ENST00000543555 | c.-116T>G | 5_prime_UTR_variant | Exon 1 of 17 | 2 | ENSP00000442697.1 | ||||
MSH2 | ENST00000406134.5 | c.-102T>G | upstream_gene_variant | 1 | ENSP00000384199.1 | |||||
MSH2 | ENST00000645506.1 | c.-102T>G | upstream_gene_variant | ENSP00000495455.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000275 AC: 3AN: 1092736Hom.: 0 Cov.: 15 AF XY: 0.00000181 AC XY: 1AN XY: 551352
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.