chr2-47414420-TAAAAAAAAAAAAA-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The ENST00000233146.7(MSH2):c.942+3_942+15delAAAAAAAAAAAAA variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00439 in 1,044,430 control chromosomes in the GnomAD database, including 107 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000233146.7 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0398 AC: 2482AN: 62390Hom.: 100 Cov.: 0
GnomAD3 exomes AF: 0.0124 AC: 648AN: 52420Hom.: 14 AF XY: 0.00933 AC XY: 262AN XY: 28096
GnomAD4 exome AF: 0.00214 AC: 2102AN: 982034Hom.: 6 AF XY: 0.00187 AC XY: 915AN XY: 488080
GnomAD4 genome AF: 0.0398 AC: 2485AN: 62396Hom.: 101 Cov.: 0 AF XY: 0.0424 AC XY: 1173AN XY: 27654
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:5
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The variant is found in HEREDICANCER,COLYNCH-HEREDIC panel(s). -
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This alteration is classified as 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. -
not specified Benign:3
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not provided Benign:2
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Breast and/or ovarian cancer Benign:1
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Lynch syndrome Benign:1
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Hereditary nonpolyposis colorectal neoplasms Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at