rs17698900

Positions:

• chr10-48738221-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.1878+2151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0924 in 152,252 control chromosomes in the GnomAD database, including 759 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 0.092 (759 hom., cov: 33)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDFY4	NM_001394531.1	c.1878+2151A>G		intron_variant		ENST00000325239.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDFY4	ENST00000325239.12	c.1878+2151A>G		intron_variant		5	NM_001394531.1	P1

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14070 AN: 152134 Hom.: 760 Cov.: 33

Gnomad AFR AF: 0.0558

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.0924 AC: 14069 AN: 152252 Hom.: 759 Cov.: 33 AF XY: 0.0885 AC XY: 6589 AN XY: 74440

Gnomad4 AFR AF: 0.0557

Gnomad4 AMR AF: 0.0912

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0449

Gnomad4 FIN AF: 0.0970

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.115

Alfa AF: 0.101 Hom.: 110

Bravo AF: 0.0912

Asia WGS AF: 0.0210 AC: 75 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.014
DANN	Benign	0.56

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: rs17698900; hg19: chr10-49946266;