chr11-125629059-C-T
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001114122.3(CHEK1):c.290-173C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0068 in 152,266 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.0068 ( 13 hom., cov: 32)
Consequence
CHEK1
NM_001114122.3 intron
NM_001114122.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.199
Genes affected
CHEK1 (HGNC:1925): (checkpoint kinase 1) The protein encoded by this gene belongs to the Ser/Thr protein kinase family. It is required for checkpoint mediated cell cycle arrest in response to DNA damage or the presence of unreplicated DNA. This protein acts to integrate signals from ATM and ATR, two cell cycle proteins involved in DNA damage responses, that also associate with chromatin in meiotic prophase I. Phosphorylation of CDC25A protein phosphatase by this protein is required for cells to delay cell cycle progression in response to double-strand DNA breaks. Several alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 11-125629059-C-T is Benign according to our data. Variant chr11-125629059-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 223666.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0068 (1035/152266) while in subpopulation AFR AF= 0.0231 (958/41546). AF 95% confidence interval is 0.0218. There are 13 homozygotes in gnomad4. There are 491 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1035 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| CHEK1 | NM_001114122.3 | c.290-173C>T | intron_variant | ENST00000438015.7 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CHEK1 | ENST00000438015.7 | c.290-173C>T | intron_variant | 5 | NM_001114122.3 | P1 |
Frequencies
GnomAD3 genomes 0.00681 AC: 1036AN: 152148Hom.: 13 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.00680 AC: 1035AN: 152266Hom.: 13 Cov.: 32 AF XY: 0.00659 AC XY: 491AN XY: 74460
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:1
| Likely benign, no assertion criteria provided | clinical testing | University of Washington Department of Laboratory Medicine, University of Washington | Dec 01, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at