chr2-47403085-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001258281.1(MSH2):c.-121C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000109 in 1,164,564 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.-121C>A | 5_prime_UTR_variant | Exon 1 of 17 | 2 | ENSP00000442697.1 | ||||
MSH2 | ENST00000406134.5 | c.-107C>A | upstream_gene_variant | 1 | ENSP00000384199.1 | |||||
MSH2 | ENST00000645506.1 | c.-107C>A | upstream_gene_variant | ENSP00000495455.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152212Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.000115 AC: 116AN: 1012234Hom.: 0 Cov.: 14 AF XY: 0.000117 AC XY: 60AN XY: 514116
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74484
ClinVar
Submissions by phenotype
not specified Uncertain:1
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Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at