10-48834274-A-G

Variant names:

• chr10-48834274-A-G
• rs735104
• NM_001394531.1:c.6663+1565A>G

Variant summary

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

The NM_001394531.1(WDFY4):​c.6663+1565A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,982 control chromosomes in the GnomAD database, including 15,537 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 0.44 (15537 hom., cov: 32)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

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]

LOC105378299 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDFY4	NM_001394531.1	c.6663+1565A>G		intron_variant	Intron 39 of 61	ENST00000325239.12	NP_001381460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDFY4	ENST00000325239.12	c.6663+1565A>G		intron_variant	Intron 39 of 61	5	NM_001394531.1	ENSP00000320563.5

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66691 AN: 151864 Hom.: 15519 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.439 AC: 66750 AN: 151982 Hom.: 15537 Cov.: 32 AF XY: 0.441 AC XY: 32759 AN XY: 74286

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.829

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.448

Alfa AF: 0.393 Hom.: 1483

Bravo AF: 0.446

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.82

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: rs735104; hg19: chr10-50042319;