NM_001258281.1:c.-116T>C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001258281.1(MSH2):c.-116T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,244,862 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001258281.1 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSH2 | ENST00000543555 | c.-116T>C | 5_prime_UTR_variant | Exon 1 of 17 | 2 | ENSP00000442697.1 | ||||
MSH2 | ENST00000406134.5 | c.-102T>C | upstream_gene_variant | 1 | ENSP00000384199.1 | |||||
MSH2 | ENST00000645506.1 | c.-102T>C | upstream_gene_variant | ENSP00000495455.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152126Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000320 AC: 35AN: 1092736Hom.: 0 Cov.: 15 AF XY: 0.0000326 AC XY: 18AN XY: 551352
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152126Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:2
The c.-102T>C variant is located in the 5' untranslated region (5’UTR) of the MSH2 gene. This variant results from a T to C substitution 102 bases upstream from the first translated codon. This nucleotide position is poorly conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at