rs10857650

Positions:

• chr10-48821978-G-A
• chr10-48821978-G-T

Variant summary

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

The NM_001394531.1(WDFY4):​c.5825-402G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,108 control chromosomes in the GnomAD database, including 5,023 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 0.23 (5023 hom., cov: 32)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDFY4	NM_001394531.1	c.5825-402G>A		intron_variant		ENST00000325239.12	NP_001381460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDFY4	ENST00000325239.12	c.5825-402G>A		intron_variant		5	NM_001394531.1	ENSP00000320563	P1
WDFY4	ENST00000374161.7	n.1464-402G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35176 AN: 151990 Hom.: 5025 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.231 AC: 35168 AN: 152108 Hom.: 5023 Cov.: 32 AF XY: 0.236 AC XY: 17557 AN XY: 74328

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.275

Alfa AF: 0.252 Hom.: 10773

Bravo AF: 0.229

Asia WGS AF: 0.441 AC: 1536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10857650; hg19: chr10-50030023;