Genetic Variant WWC1:c.2280+53_2280+60delGCTGGCTG (chr5-168431457-TCTGGCTGG-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015238.3(WWC1):c.2280+53_2280+60delGCTGGCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 1,391,104 control chromosomes in the GnomAD database, including 162,812 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 21480 hom., cov: 0)

Exomes 𝑓: 0.48 ( 141332 hom. )

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: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015238.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
WWC1	NM_015238.3	MANE Select	c.2280+53_2280+60delGCTGGCTG	intron	N/A	NP_056053.1
WWC1	NM_001161661.2		c.2280+53_2280+60delGCTGGCTG	intron	N/A	NP_001155133.1
WWC1	NM_001161662.2		c.2280+53_2280+60delGCTGGCTG	intron	N/A	NP_001155134.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
WWC1	ENST00000265293.9	TSL:1 MANE Select	c.2280+14_2280+21delCTGGCTGG	intron	N/A	ENSP00000265293.4
WWC1	ENST00000393895.7	TSL:1	c.2163+14_2163+21delCTGGCTGG	intron	N/A	ENSP00000377473.3
WWC1	ENST00000524228.5	TSL:1	c.1608+14_1608+21delCTGGCTGG	intron	N/A	ENSP00000429339.1

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

79032

AN:

148112

Hom.:

21457

Cov.:

show subpopulations

Gnomad AFR

AF:

0.604

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.560

Gnomad ASJ

AF:

0.513

Gnomad EAS

AF:

0.734

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.503

GnomAD2 exomes

AF:

0.535

AC:

67723

AN:

126504

AF XY:

0.533

show subpopulations

Gnomad AFR exome

AF:

0.549

Gnomad AMR exome

AF:

0.633

Gnomad ASJ exome

AF:

0.517

Gnomad EAS exome

AF:

0.716

Gnomad FIN exome

AF:

0.479

Gnomad NFE exome

AF:

0.470

Gnomad OTH exome

AF:

0.499

GnomAD4 exome

AF:

0.479

AC:

595789

AN:

1242884

Hom.:

141332

AF XY:

0.480

AC XY:

295899

AN XY:

616098

show subpopulations

African (AFR)

AF:

0.552

AC:

15737

AN:

28506

American (AMR)

AF:

0.592

AC:

18844

AN:

31830

Ashkenazi Jewish (ASJ)

AF:

0.476

AC:

9583

AN:

20118

East Asian (EAS)

AF:

0.653

AC:

23432

AN:

35872

South Asian (SAS)

AF:

0.518

AC:

35233

AN:

68004

European-Finnish (FIN)

AF:

0.464

AC:

16148

AN:

34796

Middle Eastern (MID)

AF:

0.408

AC:

1877

AN:

4606

European-Non Finnish (NFE)

AF:

0.465

AC:

449430

AN:

966826

Other (OTH)

AF:

0.487

AC:

25505

AN:

52326

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.549

Heterozygous variant carriers

13901

27803

41704

55606

69507

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13392

26784

40176

53568

66960

<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

AF:

0.534

AC:

79091

AN:

148220

Hom.:

21480

Cov.:

AF XY:

0.538

AC XY:

38787

AN XY:

72060

show subpopulations

African (AFR)

AF:

0.604

AC:

24303

AN:

40212

American (AMR)

AF:

0.560

AC:

8327

AN:

14860

Ashkenazi Jewish (ASJ)

AF:

0.513

AC:

1757

AN:

3428

East Asian (EAS)

AF:

0.734

AC:

3643

AN:

4962

South Asian (SAS)

AF:

0.551

AC:

2431

AN:

4410

European-Finnish (FIN)

AF:

0.472

AC:

4782

AN:

10128

Middle Eastern (MID)

AF:

0.421

AC:

122

AN:

290

European-Non Finnish (NFE)

AF:

0.480

AC:

32157

AN:

67010

Other (OTH)

AF:

0.503

AC:

1017

AN:

2020

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1747

3493

5240

6986

8733

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

690

1380

2070

2760

3450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.445

Hom.:

1588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.3

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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5-168431457-TCTGGCTGGCTGGCTGGCTGGCTGGCTGGCTGG-TCTGGCTGGCTGGCTGGCTGGCTGG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over