rs11595065

Positions:

• chr10-48769837-G-A
• chr10-48769837-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394531.1(WDFY4):​c.2554-4621G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,086 control chromosomes in the GnomAD database, including 15,472 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 0.45 (15472 hom., cov: 33)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365

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]

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 (EAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDFY4	NM_001394531.1	c.2554-4621G>A		intron_variant		ENST00000325239.12	NP_001381460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDFY4	ENST00000325239.12	c.2554-4621G>A		intron_variant		5	NM_001394531.1	ENSP00000320563	P1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68156 AN: 151968 Hom.: 15461 Cov.: 33

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.448 AC: 68208 AN: 152086 Hom.: 15472 Cov.: 33 AF XY: 0.450 AC XY: 33458 AN XY: 74344

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.530

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.499

Alfa AF: 0.449 Hom.: 32480

Bravo AF: 0.445

Asia WGS AF: 0.505 AC: 1753 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	0.34
DANN	Benign	0.73

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: rs11595065; hg19: chr10-49977882;