rs17886163
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_007194.4(CHEK2):āc.1343T>Gā(p.Ile448Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000961 in 1,612,248 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_007194.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00510 AC: 776AN: 152180Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00140 AC: 351AN: 251084Hom.: 2 AF XY: 0.000988 AC XY: 134AN XY: 135686
GnomAD4 exome AF: 0.000530 AC: 774AN: 1459950Hom.: 6 Cov.: 30 AF XY: 0.000439 AC XY: 319AN XY: 726396
GnomAD4 genome AF: 0.00510 AC: 776AN: 152298Hom.: 5 Cov.: 32 AF XY: 0.00466 AC XY: 347AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:4Other:1
- -
- -
- -
- -
- -
not provided Benign:4
CHEK2: BP4, BS1, BS2 -
This variant is associated with the following publications: (PMID: 24728327, 27595995, 21244692, 26976419, 30851065) -
- -
- -
Familial cancer of breast Benign:4
- -
- -
This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. -
- -
Hereditary cancer-predisposing syndrome Benign:4
- -
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. -
- -
- -
Li-Fraumeni syndrome 2 Benign:1
- -
Breast and/or ovarian cancer Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at