rs10508908

chr10-48765813-A-G

Variant summary

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

The NM_001394531.1(WDFY4):c.2553+5373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 151,974 control chromosomes in the GnomAD database, including 15,586 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 (15586 hom., cov: 32)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDFY4	NM_001394531.1	c.2553+5373A>G		intron_variant		ENST00000325239.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDFY4	ENST00000325239.12	c.2553+5373A>G		intron_variant		5	NM_001394531.1	P1

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68353 AN: 151856 Hom.: 15572 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.450 AC: 68405 AN: 151974 Hom.: 15586 Cov.: 32 AF XY: 0.453 AC XY: 33629 AN XY: 74262

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.496

Alfa AF: 0.442 Hom.: 17650

Bravo AF: 0.449

Asia WGS AF: 0.502 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.48
Dann	Benign	0.66

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: rs10508908; hg19: chr10-49973858;