11-125625863-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000427383.6(CHEK1):c.103C>T(p.Arg35Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 702,640 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000427383.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHEK1 | NM_001114122.3 | c.-170C>T | 5_prime_UTR_variant | 1/13 | ENST00000438015.7 | ||
LOC118567325 | NR_170378.1 | n.32G>A | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHEK1 | ENST00000438015.7 | c.-170C>T | 5_prime_UTR_variant | 1/13 | 5 | NM_001114122.3 | P1 | ||
ENST00000686400.2 | n.51G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.000841 AC: 128AN: 152260Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00123 AC: 160AN: 130584Hom.: 0 AF XY: 0.00147 AC XY: 105AN XY: 71314
GnomAD4 exome AF: 0.00128 AC: 702AN: 550262Hom.: 1 Cov.: 0 AF XY: 0.00143 AC XY: 427AN XY: 297868
GnomAD4 genome AF: 0.000840 AC: 128AN: 152378Hom.: 2 Cov.: 32 AF XY: 0.000926 AC XY: 69AN XY: 74506
ClinVar
Submissions by phenotype
CHEK1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 08, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at