5-168367771-T-C

Variant names:

• chr5-168367771-T-C
• rs1030182
• NM_015238.3:c.120-3653T>C

Variant summary

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

The NM_015238.3(WWC1):​c.120-3653T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,970 control chromosomes in the GnomAD database, including 23,831 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 0.56 (23831 hom., cov: 32)
• Consequence: WWC1 NM_015238.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351
• Publications: 5 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WWC1	NM_015238.3	c.120-3653T>C		intron_variant	Intron 1 of 22	ENST00000265293.9	NP_056053.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WWC1	ENST00000265293.9	c.120-3653T>C		intron_variant	Intron 1 of 22	1	NM_015238.3	ENSP00000265293.4
WWC1	ENST00000521089.5	c.120-3653T>C		intron_variant	Intron 1 of 22	2		ENSP00000427772.1
WWC1	ENST00000519859.1	n.186-3653T>C		intron_variant	Intron 1 of 3	4
WWC1	ENST00000523043.5	n.27-3653T>C		intron_variant	Intron 1 of 5	4

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84760 AN: 151850 Hom.: 23816 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.558 AC: 84808 AN: 151970 Hom.: 23831 Cov.: 32 AF XY: 0.559 AC XY: 41514 AN XY: 74276

African (AFR) AF: 0.495 AC: 20505 AN: 41424

American (AMR) AF: 0.643 AC: 9818 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2089 AN: 3464

East Asian (EAS) AF: 0.479 AC: 2475 AN: 5170

South Asian (SAS) AF: 0.648 AC: 3125 AN: 4826

European-Finnish (FIN) AF: 0.575 AC: 6062 AN: 10538

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.573 AC: 38946 AN: 67962

Other (OTH) AF: 0.592 AC: 1249 AN: 2110

Alfa AF: 0.576 Hom.: 50259

Bravo AF: 0.563

Asia WGS AF: 0.589 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.40
PhyloP100		-0.35
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: rs1030182; hg19: chr5-167794776;