rs10857650

Variant names:

• chr10-48821978-G-A
• rs10857650
• NM_001394531.1:c.5825-402G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

WDFY4 Gene-Disease associations (from GenCC):

• complex neurodevelopmental disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
WDFY4	NM_001394531.1	c.5825-402G>A		intron_variant	Intron 34 of 61	ENST00000325239.12	NP_001381460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDFY4	ENST00000325239.12	c.5825-402G>A		intron_variant	Intron 34 of 61	5	NM_001394531.1	ENSP00000320563.5
WDFY4	ENST00000374161.7	n.1464-402G>A		intron_variant	Intron 11 of 12	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

African (AFR) AF: 0.113 AC: 4710 AN: 41520

American (AMR) AF: 0.265 AC: 4051 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3472

East Asian (EAS) AF: 0.705 AC: 3634 AN: 5154

South Asian (SAS) AF: 0.308 AC: 1486 AN: 4824

European-Finnish (FIN) AF: 0.244 AC: 2573 AN: 10558

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16737 AN: 67976

Other (OTH) AF: 0.275 AC: 582 AN: 2114

Alfa AF: 0.246 Hom.: 21867

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
PhyloP100		-0.25
Mutation Taster		=99/1	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10857650; hg19: chr10-50030023;