5-168367771-T-C

Position:

• chr5-168367771-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
WWC1	NM_015238.3	c.120-3653T>C		intron_variant		ENST00000265293.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WWC1	ENST00000265293.9	c.120-3653T>C		intron_variant		1	NM_015238.3	P1
WWC1	ENST00000521089.5	c.120-3653T>C		intron_variant		2
WWC1	ENST00000519859.1	n.186-3653T>C		intron_variant, non_coding_transcript_variant		4
WWC1	ENST00000523043.5	n.27-3653T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.592

Alfa AF: 0.577 Hom.: 33901

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1030182; hg19: chr5-167794776;