Genetic Variant NM_015238.3:c.2280+57_2280+60dupGCTG (chr5-168431457-T-TCTGG) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_015238.3(WWC1):c.2280+57_2280+60dupGCTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0021 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0022 ( 8 hom. )

Consequence

WWC1
NM_015238.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.765

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WWC1	NM_015238.3 link	c.2280+57_2280+60dupGCTG		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+13_2280+14insCTGG		intron_variant	Intron 15 of 22	1	NM_015238.3	ENSP00000265293.4		Q8IX03-1

Frequencies

GnomAD3 genomes

AF:

0.00208

AC:

309

AN:

148352

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000921

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00283

Gnomad ASJ

AF:

0.0242

Gnomad EAS

AF:

0.00120

Gnomad SAS

AF:

0.00339

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00182

Gnomad OTH

AF:

0.00200

GnomAD2 exomes

AF:

0.00246

AC:

311

AN:

126504

AF XY:

0.00262

show subpopulations

Gnomad AFR exome

AF:

0.000983

Gnomad AMR exome

AF:

0.00169

Gnomad ASJ exome

AF:

0.0227

Gnomad EAS exome

AF:

0.00172

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00178

Gnomad OTH exome

AF:

0.00274

GnomAD4 exome

AF:

0.00219

AC:

2778

AN:

1266008

Hom.:

Cov.:

AF XY:

0.00229

AC XY:

1439

AN XY:

628320

show subpopulations

African (AFR)

AF:

0.00101

AC:

AN:

28758

American (AMR)

AF:

0.00133

AC:

AN:

32320

Ashkenazi Jewish (ASJ)

AF:

0.0286

AC:

586

AN:

20512

East Asian (EAS)

AF:

0.00186

AC:

AN:

36080

South Asian (SAS)

AF:

0.00371

AC:

258

AN:

69520

European-Finnish (FIN)

AF:

0.000393

AC:

AN:

35626

Middle Eastern (MID)

AF:

0.00449

AC:

AN:

4682

European-Non Finnish (NFE)

AF:

0.00158

AC:

1553

AN:

985202

Other (OTH)

AF:

0.00388

AC:

207

AN:

53308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

117

234

352

469

586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

136

204

272

340

<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:

0.00207

AC:

308

AN:

148462

Hom.:

Cov.:

AF XY:

0.00194

AC XY:

140

AN XY:

72194

show subpopulations

African (AFR)

AF:

0.000894

AC:

AN:

40282

American (AMR)

AF:

0.00282

AC:

AN:

14876

Ashkenazi Jewish (ASJ)

AF:

0.0242

AC:

AN:

3428

East Asian (EAS)

AF:

0.00121

AC:

AN:

4972

South Asian (SAS)

AF:

0.00339

AC:

AN:

4420

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10164

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.00182

AC:

122

AN:

67104

Other (OTH)

AF:

0.00198

AC:

AN:

2024

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00552

Hom.:

1588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.77

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over