4-10088139-C-T

Position:

• chr4-10088139-C-T

Variant summary

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

The NM_017491.5(WDR1):​c.717+154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 900,388 control chromosomes in the GnomAD database, including 44,245 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 0.30 (7187 hom., cov: 32)
  • Exomes 𝑓: 0.31 (37058 hom.)
• Consequence: WDR1 NM_017491.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831

Genes affected

WDR1 (HGNC:12754): (WD repeat domain 1) This gene encodes a protein containing 9 WD repeats. WD repeats are approximately 30- to 40-amino acid domains containing several conserved residues, mostly including a trp-asp at the C-terminal end. WD domains are involved in protein-protein interactions. The encoded protein may help induce the disassembly of actin filaments. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

WDR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR1	NM_017491.5	c.717+154G>A		intron_variant		ENST00000499869.7	NP_059830.1
WDR1	NM_005112.5	c.297+154G>A		intron_variant			NP_005103.2
WDR1	XM_017008880.3	c.876+154G>A		intron_variant			XP_016864369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR1	ENST00000499869.7	c.717+154G>A		intron_variant		5	NM_017491.5	ENSP00000427687.1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45357 AN: 151924 Hom.: 7167 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.316

GnomAD4 exome AF: 0.308 AC: 230734 AN: 748346 Hom.: 37058 AF XY: 0.308 AC XY: 118954 AN XY: 385892

Gnomad4 AFR exome AF: 0.242

Gnomad4 AMR exome AF: 0.356

Gnomad4 ASJ exome AF: 0.417

Gnomad4 EAS exome AF: 0.527

Gnomad4 SAS exome AF: 0.301

Gnomad4 FIN exome AF: 0.307

Gnomad4 NFE exome AF: 0.290

Gnomad4 OTH exome AF: 0.323

GnomAD4 genome AF: 0.299 AC: 45409 AN: 152042 Hom.: 7187 Cov.: 32 AF XY: 0.301 AC XY: 22399 AN XY: 74320

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.325

Alfa AF: 0.272 Hom.: 2983

Bravo AF: 0.305

Asia WGS AF: 0.410 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.62

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: rs2241480; hg19: chr4-10089763;