rs2671692

Positions:

• chr10-48889774-G-A
• chr10-48889774-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.7168-805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,070 control chromosomes in the GnomAD database, including 23,040 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 0.54 (23040 hom., cov: 33)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

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]

(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 (NFE) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDFY4	NM_001394531.1	c.7168-805G>A		intron_variant		ENST00000325239.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDFY4	ENST00000325239.12	c.7168-805G>A		intron_variant		5	NM_001394531.1	P1
	ENST00000430438.1	n.174-5434C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82061 AN: 151952 Hom.: 23013 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.540 AC: 82138 AN: 152070 Hom.: 23040 Cov.: 33 AF XY: 0.536 AC XY: 39850 AN XY: 74340

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.514

Alfa AF: 0.594 Hom.: 33585

Bravo AF: 0.534

Asia WGS AF: 0.426 AC: 1479 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	1.3
DANN	Benign	0.69

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: rs2671692; hg19: chr10-50097819;