rs9535720

Variant names:

• chr13-51620808-T-C
• rs9535720
• NM_052950.4:c.137+35984T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
WDFY2	NM_052950.4	c.137+35984T>C		intron_variant	Intron 1 of 11	ENST00000298125.7	NP_443182.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDFY2	ENST00000298125.7	c.137+35984T>C		intron_variant	Intron 1 of 11	1	NM_052950.4	ENSP00000298125.4

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

African (AFR) AF: 0.386 AC: 15983 AN: 41394

American (AMR) AF: 0.530 AC: 8092 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2304 AN: 5108

South Asian (SAS) AF: 0.518 AC: 2494 AN: 4812

European-Finnish (FIN) AF: 0.487 AC: 5136 AN: 10536

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28321 AN: 67926

Other (OTH) AF: 0.398 AC: 840 AN: 2112

Alfa AF: 0.416 Hom.: 26790

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
PhyloP100		-0.63
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: rs9535720; hg19: chr13-52194944;