rs9535720

chr13-51620808-T-C

Variant summary

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

The NM_052950.4(WDFY2):c.137+35984T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,816 control chromosomes in the GnomAD database, including 14,009 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 0.43 (14009 hom., cov: 30)
• Consequence: WDFY2 NM_052950.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.625

Genes affected

WDFY2 (HGNC:20482): (WD repeat and FYVE domain containing 2) This gene encodes a protein that contains two WD domains and an FYVE zinc finger region. The function of this gene is unknown. An alternatively spliced transcript variant of this gene may exist. [provided by RefSeq, Jul 2008]

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 (AMR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDFY2	NM_052950.4	c.137+35984T>C		intron_variant		ENST00000298125.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDFY2	ENST00000298125.7	c.137+35984T>C		intron_variant		1	NM_052950.4	P1

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64600 AN: 151698 Hom.: 13989 Cov.: 30

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.426 AC: 64675 AN: 151816 Hom.: 14009 Cov.: 30 AF XY: 0.433 AC XY: 32140 AN XY: 74180

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.398

Alfa AF: 0.416 Hom.: 18440

Bravo AF: 0.423

Asia WGS AF: 0.490 AC: 1703 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	1.5
Dann	Benign	0.39

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: rs9535720; hg19: chr13-52194944;