chr11-125625780-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000427383.6(CHEK1):c.20A>T(p.Lys7Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00208 in 694,784 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
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.-253A>T | 5_prime_UTR_variant | 1/13 | ENST00000438015.7 | ||
LOC118567325 | NR_170378.1 | n.115T>A | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHEK1 | ENST00000438015.7 | c.-253A>T | 5_prime_UTR_variant | 1/13 | 5 | NM_001114122.3 | P1 | ||
ENST00000686400.2 | n.134T>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00648 AC: 986AN: 152184Hom.: 16 Cov.: 33
GnomAD3 exomes AF: 0.00134 AC: 175AN: 130182Hom.: 4 AF XY: 0.00125 AC XY: 89AN XY: 71050
GnomAD4 exome AF: 0.000841 AC: 456AN: 542482Hom.: 6 Cov.: 0 AF XY: 0.000736 AC XY: 215AN XY: 292160
GnomAD4 genome AF: 0.00647 AC: 986AN: 152302Hom.: 16 Cov.: 33 AF XY: 0.00620 AC XY: 462AN XY: 74488
ClinVar
Submissions by phenotype
CHEK1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 23, 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