rs2947344

chr10-48776645-G-A

Variant summary

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

The NM_001394531.1(WDFY4):c.2864-105G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 1,194,218 control chromosomes in the GnomAD database, including 304,342 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 0.60 (30218 hom., cov: 34)
  • Exomes 𝑓: 0.72 (274124 hom.)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28

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 (NFE) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDFY4	NM_001394531.1	c.2864-105G>A		intron_variant		ENST00000325239.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDFY4	ENST00000325239.12	c.2864-105G>A		intron_variant		5	NM_001394531.1	P1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91107 AN: 152080 Hom.: 30218 Cov.: 34

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.596

GnomAD4 exome AF: 0.720 AC: 749914 AN: 1042020 Hom.: 274124 AF XY: 0.721 AC XY: 369802 AN XY: 513094

Gnomad4 AFR exome AF: 0.281

Gnomad4 AMR exome AF: 0.751

Gnomad4 ASJ exome AF: 0.694

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.720

Gnomad4 FIN exome AF: 0.715

Gnomad4 NFE exome AF: 0.744

Gnomad4 OTH exome AF: 0.677

GnomAD4 genome AF: 0.599 AC: 91115 AN: 152198 Hom.: 30218 Cov.: 34 AF XY: 0.602 AC XY: 44773 AN XY: 74406

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.598

Alfa AF: 0.714 Hom.: 79831

Bravo AF: 0.585

Asia WGS AF: 0.560 AC: 1951 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	0.083
Dann	Benign	0.55

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: rs2947344; hg19: chr10-49984690;