rs1913517

Variant names:

• chr10-48911009-A-G
• rs1913517
• NM_001394531.1:c.7586+9146A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-48911009-A-G
• chr10-48911009-A-T

Variant summary

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

The NM_001394531.1(WDFY4):​c.7586+9146A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 582,662 control chromosomes in the GnomAD database, including 74,543 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 (22581 hom., cov: 33)
  • Exomes 𝑓: 0.49 (51962 hom.)
• Consequence: WDFY4 NM_001394531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13
• Publications: 52 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394531.1. 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+9146A>G		intron	N/A	NP_001381460.1	Q6ZS81-1
	LRRC18	NM_001378102.1	MANE Select	c.765-751T>C		intron	N/A	NP_001365031.1	Q8N456-1
	WDFY4	NM_020945.2		c.7586+9146A>G		intron	N/A	NP_065996.1	Q6ZS81-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDFY4	ENST00000325239.12	TSL:5 MANE Select	c.7586+9146A>G		intron	N/A	ENSP00000320563.5	Q6ZS81-1
	LRRC18	ENST00000374160.8	TSL:1 MANE Select	c.765-751T>C		intron	N/A	ENSP00000363275.3	Q8N456-1
	WDFY4	ENST00000858472.1		c.7586+9146A>G		intron	N/A	ENSP00000528531.1

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81848 AN: 152034 Hom.: 22563 Cov.: 33

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.597

GnomAD4 exome AF: 0.491 AC: 211244 AN: 430510 Hom.: 51962 AF XY: 0.491 AC XY: 99582 AN XY: 202860

African (AFR) AF: 0.654 AC: 5211 AN: 7970

American (AMR) AF: 0.525 AC: 254 AN: 484

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 1741 AN: 2778

East Asian (EAS) AF: 0.760 AC: 1451 AN: 1908

South Asian (SAS) AF: 0.622 AC: 5495 AN: 8828

European-Finnish (FIN) AF: 0.556 AC: 90 AN: 162

Middle Eastern (MID) AF: 0.704 AC: 603 AN: 856

European-Non Finnish (NFE) AF: 0.480 AC: 188750 AN: 393512

Other (OTH) AF: 0.546 AC: 7649 AN: 14012

GnomAD4 genome AF: 0.538 AC: 81907 AN: 152152 Hom.: 22581 Cov.: 33 AF XY: 0.543 AC XY: 40422 AN XY: 74380

African (AFR) AF: 0.624 AC: 25888 AN: 41476

American (AMR) AF: 0.505 AC: 7735 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.608 AC: 2109 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3724 AN: 5186

South Asian (SAS) AF: 0.620 AC: 2986 AN: 4818

European-Finnish (FIN) AF: 0.514 AC: 5437 AN: 10586

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32112 AN: 67998

Other (OTH) AF: 0.593 AC: 1251 AN: 2108

Alfa AF: 0.496 Hom.: 90097

Bravo AF: 0.540

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.26
PhyloP100		-3.1
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: rs1913517; hg19: chr10-50119054;