rs10857619

Positions:

• chr10-48699268-A-G
• chr10-48699268-A-T

Variant summary

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

The NM_001394531.1(WDFY4):​c.-17-10448A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 151,992 control chromosomes in the GnomAD database, including 23,158 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 0.55 (23158 hom., cov: 32)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

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=-0.91).
• 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.-17-10448A>G		intron_variant		ENST00000325239.12	NP_001381460.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDFY4	ENST00000325239.12	c.-17-10448A>G		intron_variant		5	NM_001394531.1	ENSP00000320563	P1
WDFY4	ENST00000360890.6	c.-17-10448A>G		intron_variant		1		ENSP00000354141

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83071 AN: 151874 Hom.: 23154 Cov.: 32

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.547 AC: 83102 AN: 151992 Hom.: 23158 Cov.: 32 AF XY: 0.547 AC XY: 40655 AN XY: 74280

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.705

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.516

Alfa AF: 0.569 Hom.: 48400

Bravo AF: 0.547

Asia WGS AF: 0.585 AC: 2036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10857619; hg19: chr10-49907313;