chr10-48917927-C-T

Variant names:

• chr10-48917927-C-T
• rs2663056
• NM_001394531.1:c.7586+16064C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020945.2(WDFY4):​c.7586+16064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,124 control chromosomes in the GnomAD database, including 3,506 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 0.20 (3506 hom., cov: 33)
• Consequence: WDFY4 NM_020945.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 5 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]

LRRC18 (HGNC:23199): (leucine rich repeat containing 18) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000241577 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020945.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDFY4	NM_001394531.1	MANE Select	c.7586+16064C>T		intron	N/A	NP_001381460.1
	LRRC18	NM_001378102.1	MANE Select	c.-77-3695G>A		intron	N/A	NP_001365031.1
	WDFY4	NM_020945.2		c.7586+16064C>T		intron	N/A	NP_065996.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDFY4	ENST00000325239.12	TSL:5 MANE Select	c.7586+16064C>T		intron	N/A	ENSP00000320563.5
	LRRC18	ENST00000374160.8	TSL:1 MANE Select	c.-77-3695G>A		intron	N/A	ENSP00000363275.3
	WDFY4	ENST00000858472.1		c.7586+16064C>T		intron	N/A	ENSP00000528531.1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30933 AN: 152006 Hom.: 3506 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.203 AC: 30934 AN: 152124 Hom.: 3506 Cov.: 33 AF XY: 0.197 AC XY: 14657 AN XY: 74354

African (AFR) AF: 0.161 AC: 6679 AN: 41500

American (AMR) AF: 0.147 AC: 2243 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5188

South Asian (SAS) AF: 0.0813 AC: 392 AN: 4822

European-Finnish (FIN) AF: 0.227 AC: 2398 AN: 10554

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17973 AN: 67986

Other (OTH) AF: 0.174 AC: 367 AN: 2108

Alfa AF: 0.236 Hom.: 13892

Bravo AF: 0.197

Asia WGS AF: 0.0590 AC: 206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.2
DANN	Benign	0.76
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2663056; hg19: chr10-50125972;