10-48975692-T-C

Position:

• chr10-48975692-T-C

Variant summary

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

The NM_001394531.1(WDFY4):​c.9108+651T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,062 control chromosomes in the GnomAD database, including 54,645 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 0.83 (54645 hom., cov: 31)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDFY4	NM_001394531.1	c.9108+651T>C		intron_variant		ENST00000325239.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDFY4	ENST00000325239.12	c.9108+651T>C		intron_variant		5	NM_001394531.1	P1
WDFY4	ENST00000465910.5	n.3742+651T>C		intron_variant, non_coding_transcript_variant		2
WDFY4	ENST00000497480.1	n.604+651T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126730 AN: 151944 Hom.: 54642 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.944

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.834 AC: 126768 AN: 152062 Hom.: 54645 Cov.: 31 AF XY: 0.836 AC XY: 62168 AN XY: 74344

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.944

Gnomad4 NFE AF: 0.935

Gnomad4 OTH AF: 0.847

Alfa AF: 0.910 Hom.: 24352

Bravo AF: 0.818

Asia WGS AF: 0.906 AC: 3151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.72

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: rs1317894; hg19: chr10-50183737;