NM_000251.3:c.942+28_942+29delAA
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1
The NM_000251.3(MSH2):c.942+28_942+29delAA variant causes a intron change. The variant allele was found at a frequency of 0.179 in 965,430 control chromosomes in the GnomAD database, including 1,339 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000251.3 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 9816AN: 62568Hom.: 372 Cov.: 0 FAILED QC
GnomAD3 exomes AF: 0.0914 AC: 4790AN: 52420Hom.: 14 AF XY: 0.0872 AC XY: 2450AN XY: 28096
GnomAD4 exome AF: 0.179 AC: 173109AN: 965430Hom.: 1339 AF XY: 0.176 AC XY: 84578AN XY: 479320
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.157 AC: 9812AN: 62570Hom.: 371 Cov.: 0 AF XY: 0.160 AC XY: 4436AN XY: 27718
ClinVar
Submissions by phenotype
not specified Benign:3
- -
- -
- -
Lynch syndrome Uncertain:2
- -
- -
Lynch syndrome 1 Uncertain:1Benign:1
- -
- -
MSH2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Breast and/or ovarian cancer Benign:1
- -
not provided Benign:1
- -
Hereditary nonpolyposis colorectal neoplasms Benign:1
- -
Hereditary cancer-predisposing syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at