dbSNP rs2271565: WDFY4:p.Cys3072Cys (chr10-48976904-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_001394531.1(WDFY4):c.9216C>T(p.Cys3072Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 1,537,308 control chromosomes in the GnomAD database, including 179,851 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.38 ( 12696 hom., cov: 33)

Exomes 𝑓: 0.48 ( 167155 hom. )

Consequence

WDFY4
NM_001394531.1 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.41

Variant links:

Genes affected

WDFY4 (HGNC:29323): (WDFY family member 4) Predicted to be involved in autophagy. Predicted to act upstream of or within with a positive effect on CD8-positive, alpha-beta T cell activation. Predicted to act upstream of or within antigen processing and presentation and cellular response to virus. Predicted to be located in early endosome and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

WDFY4 links:

ENSG00000233665 (HGNC:):

ENSG00000233665 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BP6

Variant 10-48976904-C-T is Benign according to our data. Variant chr10-48976904-C-T is described in ClinVar as [Benign]. Clinvar id is 3059895.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.41 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDFY4	NM_001394531.1 link	c.9216C>T	p.Cys3072Cys	synonymous_variant	Exon 59 of 62	ENST00000325239.12	NP_001381460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDFY4	ENST00000325239.12 link	c.9216C>T	p.Cys3072Cys	synonymous_variant	Exon 59 of 62	5	NM_001394531.1	ENSP00000320563.5		Q6ZS81-1

Frequencies

GnomAD3 genomes

AF:

0.376

AC:

57128

AN:

152060

Hom.:

12696

Cov.:

show subpopulations

Gnomad AFR

AF:

0.129

Gnomad AMI

AF:

0.498

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.416

Gnomad EAS

AF:

0.322

Gnomad SAS

AF:

0.475

Gnomad FIN

AF:

0.408

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.508

Gnomad OTH

AF:

0.380

GnomAD3 exomes

AF:

0.429

AC:

62188

AN:

144972

Hom.:

14186

AF XY:

0.438

AC XY:

33700

AN XY:

76922

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.377

Gnomad ASJ exome

AF:

0.417

Gnomad EAS exome

AF:

0.314

Gnomad SAS exome

AF:

0.463

Gnomad FIN exome

AF:

0.417

Gnomad NFE exome

AF:

0.503

Gnomad OTH exome

AF:

0.443

GnomAD4 exome

AF:

0.484

AC:

670985

AN:

1385130

Hom.:

167155

Cov.:

AF XY:

0.484

AC XY:

330760

AN XY:

682862

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.385

Gnomad4 ASJ exome

AF:

0.422

Gnomad4 EAS exome

AF:

0.249

Gnomad4 SAS exome

AF:

0.470

Gnomad4 FIN exome

AF:

0.424

Gnomad4 NFE exome

AF:

0.513

Gnomad4 OTH exome

AF:

0.457

GnomAD4 genome

AF:

0.375

AC:

57130

AN:

152178

Hom.:

12696

Cov.:

AF XY:

0.375

AC XY:

27866

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.129

Gnomad4 AMR

AF:

0.402

Gnomad4 ASJ

AF:

0.416

Gnomad4 EAS

AF:

0.322

Gnomad4 SAS

AF:

0.474

Gnomad4 FIN

AF:

0.408

Gnomad4 NFE

AF:

0.508

Gnomad4 OTH

AF:

0.384

Alfa

AF:

0.452

Hom.:

12089

Bravo

AF:

0.361

Asia WGS

AF:

0.427

AC:

1480

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

WDFY4-related disorder

Benign:1

Jun 28, 2023

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.84

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over