rs1476640

Positions:

• chr7-141712510-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001105558.1(WEE2):​c.343-1699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,936 control chromosomes in the GnomAD database, including 27,293 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 0.59 (27293 hom., cov: 32)
• Consequence: WEE2 NM_001105558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

WEE2 (HGNC:19684): (WEE2 oocyte meiosis inhibiting kinase) Predicted to enable protein tyrosine kinase activity. Predicted to be involved in several processes, including female pronucleus assembly; negative regulation of oocyte maturation; and regulation of meiosis I. Located in cytosol; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

WEE2-AS1 (HGNC:48669): (WEE2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WEE2	NM_001105558.1	c.343-1699T>C		intron_variant		ENST00000397541.6	NP_001099028.1
WEE2-AS1	NR_015392.1	n.842+1679A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WEE2	ENST00000397541.6	c.343-1699T>C		intron_variant		1	NM_001105558.1	ENSP00000380675	P1
WEE2-AS1	ENST00000665340.1	n.618-6753A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90333 AN: 151818 Hom.: 27290 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.571

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.595 AC: 90363 AN: 151936 Hom.: 27293 Cov.: 32 AF XY: 0.593 AC XY: 43983 AN XY: 74220

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.568

Alfa AF: 0.589 Hom.: 2928

Bravo AF: 0.593

Asia WGS AF: 0.482 AC: 1680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.82
DANN	Benign	0.60

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: rs1476640; hg19: chr7-141412310;