rs1004407

Positions:

• chr10-48694080-C-A

Variant summary

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

The NM_001394531.1(WDFY4):​c.-18+9079C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 152,110 control chromosomes in the GnomAD database, including 11,532 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 0.38 (11532 hom., cov: 32)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDFY4	NM_001394531.1	c.-18+9079C>A		intron_variant		ENST00000325239.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDFY4	ENST00000325239.12	c.-18+9079C>A		intron_variant		5	NM_001394531.1	P1
WDFY4	ENST00000360890.6	c.-18+9079C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57564 AN: 151990 Hom.: 11507 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.379 AC: 57636 AN: 152110 Hom.: 11532 Cov.: 32 AF XY: 0.373 AC XY: 27769 AN XY: 74352

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.403

Alfa AF: 0.365 Hom.: 2315

Bravo AF: 0.388

Asia WGS AF: 0.343 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1004407; hg19: chr10-49902125;