chr11-125625851-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000427383.6(CHEK1):āc.91C>Gā(p.Pro31Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0763 in 702,562 control chromosomes in the GnomAD database, including 3,088 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 Benign (ā ).
Frequency
Consequence
ENST00000427383.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHEK1 | NM_001114122.3 | c.-182C>G | 5_prime_UTR_variant | 1/13 | ENST00000438015.7 | ||
LOC118567325 | NR_170378.1 | n.44G>C | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHEK1 | ENST00000438015.7 | c.-182C>G | 5_prime_UTR_variant | 1/13 | 5 | NM_001114122.3 | P1 | ||
ENST00000686400.2 | n.63G>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.112 AC: 17100AN: 152202Hom.: 1465 Cov.: 33
GnomAD3 exomes AF: 0.0657 AC: 8588AN: 130658Hom.: 416 AF XY: 0.0641 AC XY: 4570AN XY: 71344
GnomAD4 exome AF: 0.0663 AC: 36470AN: 550242Hom.: 1620 Cov.: 0 AF XY: 0.0639 AC XY: 19036AN XY: 297860
GnomAD4 genome AF: 0.112 AC: 17131AN: 152320Hom.: 1468 Cov.: 33 AF XY: 0.109 AC XY: 8146AN XY: 74486
ClinVar
Submissions by phenotype
CHEK1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 30, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at