10-48728291-C-T

Variant names:

• chr10-48728291-C-T
• rs11101442
• NM_001394531.1:c.971+632C>T

Variant summary

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

The NM_001394531.1(WDFY4):​c.971+632C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,164 control chromosomes in the GnomAD database, including 7,074 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 0.29 (7074 hom., cov: 33)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDFY4	NM_001394531.1	c.971+632C>T		intron_variant	Intron 7 of 61	ENST00000325239.12	NP_001381460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDFY4	ENST00000325239.12	c.971+632C>T		intron_variant	Intron 7 of 61	5	NM_001394531.1	ENSP00000320563.5
WDFY4	ENST00000360890.6	c.971+632C>T		intron_variant	Intron 7 of 10	1		ENSP00000354141.2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43853 AN: 152046 Hom.: 7082 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.288 AC: 43856 AN: 152164 Hom.: 7074 Cov.: 33 AF XY: 0.295 AC XY: 21949 AN XY: 74396

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.319

Alfa AF: 0.325 Hom.: 14953

Bravo AF: 0.270

Asia WGS AF: 0.381 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.013
DANN	Benign	0.53

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: rs11101442; hg19: chr10-49936336;