rs768055

Variant names:

• chr7-141713251-C-A
• rs768055
• NM_001105558.1:c.343-958C>A

Variant summary

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

The NM_001105558.1(WEE2):​c.343-958C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,910 control chromosomes in the GnomAD database, including 14,022 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 0.43 (14022 hom., cov: 32)
• Consequence: WEE2 NM_001105558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 13 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WEE2	NM_001105558.1	c.343-958C>A		intron_variant	Intron 1 of 11	ENST00000397541.6	NP_001099028.1
WEE2-AS1	NR_015392.1	n.842+938G>T		intron_variant	Intron 6 of 6
WEE2-AS1	NR_199840.1	n.1109+938G>T		intron_variant	Intron 4 of 4
WEE2-AS1	NR_199841.1	n.924-7494G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WEE2	ENST00000397541.6	c.343-958C>A		intron_variant	Intron 1 of 11	1	NM_001105558.1	ENSP00000380675.2

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64601 AN: 151792 Hom.: 14017 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.425 AC: 64620 AN: 151910 Hom.: 14022 Cov.: 32 AF XY: 0.424 AC XY: 31483 AN XY: 74250

African (AFR) AF: 0.486 AC: 20096 AN: 41392

American (AMR) AF: 0.315 AC: 4814 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3466

East Asian (EAS) AF: 0.248 AC: 1280 AN: 5164

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4812

European-Finnish (FIN) AF: 0.480 AC: 5058 AN: 10540

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28643 AN: 67954

Other (OTH) AF: 0.401 AC: 846 AN: 2110

Alfa AF: 0.413 Hom.: 21505

Bravo AF: 0.414

Asia WGS AF: 0.298 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		0.16
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: rs768055; hg19: chr7-141413051;