rs3765501

Positions:

• chr1-117937126-G-A
• chr1-117937126-G-C

Variant summary

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

The ENST00000349139.6(WDR3):​c.500+239G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,646 control chromosomes in the GnomAD database, including 17,590 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 0.48 (17590 hom., cov: 31)
• Consequence: WDR3 ENST00000349139.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.713

Genes affected

WDR3 (HGNC:12755): (WD repeat domain 3) This gene encodes a nuclear protein containing 10 WD repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, which usually include a trp-asp at the C-terminal end. Proteins belonging to the WD repeat family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR3	NM_006784.3	c.500+239G>A		intron_variant		ENST00000349139.6	NP_006775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR3	ENST00000349139.6	c.500+239G>A		intron_variant		1	NM_006784.3	ENSP00000308179	P1
WDR3	ENST00000369441.7	c.*387+239G>A		intron_variant		1		ENSP00000358449
WDR3	ENST00000471680.1	n.682+239G>A		intron_variant, non_coding_transcript_variant		5
WDR3	ENST00000487202.5	n.601+239G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72632 AN: 151528 Hom.: 17558 Cov.: 31

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.480 AC: 72716 AN: 151646 Hom.: 17590 Cov.: 31 AF XY: 0.479 AC XY: 35485 AN XY: 74114

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.476

Alfa AF: 0.465 Hom.: 2540

Bravo AF: 0.474

Asia WGS AF: 0.591 AC: 2053 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.031
DANN	Benign	0.21

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: rs3765501; hg19: chr1-118479749;