rs11042431

Variant names:

• chr11-9585129-A-G
• rs11042431
• NM_003390.4:c.1289-129A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-9585129-A-G
• chr11-9585129-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003390.4(WEE1):​c.1289-129A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 734,756 control chromosomes in the GnomAD database, including 9,550 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.15 (1794 hom., cov: 32)
  • Exomes 𝑓: 0.16 (7756 hom.)
• Consequence: WEE1 NM_003390.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105
• Publications: 1 publications found

Genes affected

WEE1 (HGNC:12761): (WEE1 G2 checkpoint kinase) This gene encodes a nuclear protein, which is a tyrosine kinase belonging to the Ser/Thr family of protein kinases. This protein catalyzes the inhibitory tyrosine phosphorylation of CDC2/cyclin B kinase, and appears to coordinate the transition between DNA replication and mitosis by protecting the nucleus from cytoplasmically activated CDC2 kinase. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003390.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WEE1	NM_003390.4	MANE Select	c.1289-129A>G		intron	N/A	NP_003381.1	P30291-1
	WEE1	NM_001143976.2		c.647-129A>G		intron	N/A	NP_001137448.1	P30291-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WEE1	ENST00000450114.7	TSL:1 MANE Select	c.1289-129A>G		intron	N/A	ENSP00000402084.2	P30291-1
	WEE1	ENST00000919884.1		c.1340-129A>G		intron	N/A	ENSP00000589943.1
	WEE1	ENST00000919883.1		c.1289-129A>G		intron	N/A	ENSP00000589942.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23370 AN: 151984 Hom.: 1790 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.160 AC: 93061 AN: 582654 Hom.: 7756 AF XY: 0.158 AC XY: 48359 AN XY: 306376

African (AFR) AF: 0.124 AC: 1842 AN: 14842

American (AMR) AF: 0.143 AC: 2896 AN: 20206

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 1705 AN: 14998

East Asian (EAS) AF: 0.243 AC: 8079 AN: 33250

South Asian (SAS) AF: 0.131 AC: 6478 AN: 49536

European-Finnish (FIN) AF: 0.184 AC: 7043 AN: 38230

Middle Eastern (MID) AF: 0.131 AC: 290 AN: 2218

European-Non Finnish (NFE) AF: 0.158 AC: 60052 AN: 379152

Other (OTH) AF: 0.155 AC: 4676 AN: 30222

GnomAD4 genome AF: 0.154 AC: 23379 AN: 152102 Hom.: 1794 Cov.: 32 AF XY: 0.157 AC XY: 11688 AN XY: 74352

African (AFR) AF: 0.128 AC: 5318 AN: 41516

American (AMR) AF: 0.172 AC: 2623 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 396 AN: 3470

East Asian (EAS) AF: 0.208 AC: 1077 AN: 5172

South Asian (SAS) AF: 0.131 AC: 630 AN: 4824

European-Finnish (FIN) AF: 0.188 AC: 1987 AN: 10562

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10831 AN: 67984

Other (OTH) AF: 0.128 AC: 270 AN: 2108

Alfa AF: 0.0905 Hom.: 160

Bravo AF: 0.148

Asia WGS AF: 0.159 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.53
PhyloP100		0.10
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11042431; hg19: chr11-9606676;