chr11-125625837-A-G

Variant names:

• chr11-125625837-A-G
• rs565780672
• ENST00000427383.6:c.77A>G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_Strong BP6 BS2

The ENST00000427383.6(CHEK1):​c.77A>G​(p.Asn26Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00309 in 702,610 control chromosomes in the GnomAD database, including 6 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 (no stars). Synonymous variant affecting the same amino acid position (i.e. N26N) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.0025 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0033 (6 hom.)
• Consequence: CHEK1 ENST00000427383.6 missense
• Clinical Significance: Benign no assertion criteria provided B:1
• Conservation: PhyloP100: -2.58

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]

ENSG00000288907 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.004249066).
• BP6: Variant 11-125625837-A-G is Benign according to our data. Variant chr11-125625837-A-G is described in ClinVar as [Benign]. Clinvar id is 3043887.Status of the report is no_assertion_criteria_provided, 0 stars.
• BS2: High AC in GnomAd4 at 374 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHEK1	NM_001114122.3	c.-196A>G		5_prime_UTR_variant	Exon 1 of 13	ENST00000438015.7	NP_001107594.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHEK1	ENST00000438015	c.-196A>G		5_prime_UTR_variant	Exon 1 of 13	5	NM_001114122.3	ENSP00000388648.1

Frequencies

GnomAD3 genomes AF: 0.00245 AC: 373 AN: 152256 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000675

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00310

Gnomad OTH AF: 0.00143

GnomAD3 exomes AF: 0.00244 AC: 319 AN: 130710 Hom.: 1 AF XY: 0.00254 AC XY: 181 AN XY: 71364

Gnomad AFR exome AF: 0.000493

Gnomad AMR exome AF: 0.000657

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00210

Gnomad FIN exome AF: 0.00985

Gnomad NFE exome AF: 0.00376

Gnomad OTH exome AF: 0.00299

GnomAD4 exome AF: 0.00326 AC: 1794 AN: 550236 Hom.: 6 Cov.: 0 AF XY: 0.00324 AC XY: 964 AN XY: 297858

Gnomad4 AFR exome AF: 0.000506

Gnomad4 AMR exome AF: 0.000835

Gnomad4 ASJ exome AF: 0.0000499

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00245

Gnomad4 FIN exome AF: 0.0110

Gnomad4 NFE exome AF: 0.00362

Gnomad4 OTH exome AF: 0.00275

GnomAD4 genome AF: 0.00245 AC: 374 AN: 152374 Hom.: 0 Cov.: 33 AF XY: 0.00264 AC XY: 197 AN XY: 74512

Gnomad4 AFR AF: 0.000673

Gnomad4 AMR AF: 0.000588

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00103

Gnomad4 FIN AF: 0.0111

Gnomad4 NFE AF: 0.00310

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00215 Hom.: 0

Bravo AF: 0.00181

TwinsUK AF: 0.00162 AC: 6

ALSPAC AF: 0.00234 AC: 9

ExAC AF: 0.00149 AC: 24

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

CHEK1-related disorder Benign:1

Nov 08, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.49	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	0.27
DANN	Benign	0.89
DEOGEN2	Benign	0.0049	T
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.4
FATHMM_MKL	Benign	0.0075	N
LIST_S2	Benign	0.52	T
MetaRNN	Benign	0.0042	T
MetaSVM	Benign	-1.0	T
PROVEAN	Benign	0.65	N
REVEL	Benign	0.095
Sift	Pathogenic	0.0	D
Sift4G	Pathogenic	0.0	D
Polyphen		0.0	B
Vest4		0.092
MVP		0.32
ClinPred		0.038	T
GERP RS		-4.1
gMVP		0.094

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs565780672; hg19: chr11-125495732; COSMIC: COSV54024147; COSMIC: COSV54024147;