Genetic Variant WWC1:c.2280+33_2280+60delGCTGGCTGGCTGGCTGGCTGGCTGGCTG (chr5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGG-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_015238.3(WWC1):c.2280+33_2280+60delGCTGGCTGGCTGGCTGGCTGGCTGGCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000395 in 1,266,092 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000039 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

WWC1
NM_015238.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.31

Publications

2 publications found

Variant links:

Genes affected

WWC1 (HGNC:29435): (WW and C2 domain containing 1) The protein encoded by this gene is a cytoplasmic phosphoprotein that interacts with PRKC-zeta and dynein light chain-1. Alleles of this gene have been found that enhance memory in some individuals. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

WWC1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WWC1	NM_015238.3 link	c.2280+33_2280+60delGCTGGCTGGCTGGCTGGCTGGCTGGCTG		intron_variant	Intron 15 of 22	ENST00000265293.9	NP_056053.1	Q8IX03-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WWC1	ENST00000265293.9 link	c.2280+14_2280+41delCTGGCTGGCTGGCTGGCTGGCTGGCTGG		intron_variant	Intron 15 of 22	1	NM_015238.3	ENSP00000265293.4		Q8IX03-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

148354

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000395

AC:

AN:

1266092

Hom.:

AF XY:

0.00000318

AC XY:

AN XY:

628358

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

28758

American (AMR)

AF:

0.00

AC:

AN:

32320

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20524

East Asian (EAS)

AF:

0.0000277

AC:

AN:

36082

South Asian (SAS)

AF:

0.0000144

AC:

AN:

69526

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35626

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4682

European-Non Finnish (NFE)

AF:

0.00000304

AC:

AN:

985258

Other (OTH)

AF:

0.00

AC:

AN:

53316

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.655

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

148354

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

72076

African (AFR)

AF:

0.00

AC:

AN:

40166

American (AMR)

AF:

0.00

AC:

AN:

14856

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3430

East Asian (EAS)

AF:

0.00

AC:

AN:

4984

South Asian (SAS)

AF:

0.00

AC:

AN:

4424

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10164

Middle Eastern (MID)

AF:

0.00

AC:

AN:

312

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67114

Other (OTH)

AF:

0.00

AC:

AN:

2002

Alfa

AF:

0.00

Hom.:

1588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.3

Splicing

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

Publications

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5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGG-TCTGG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over