rs9295009

Variant names:

• chr6-169579060-C-T
• rs9295009
• NM_182552.5:c.2523+3776G>A

Variant summary

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

The NM_182552.5(WDR27):​c.2523+3776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,040 control chromosomes in the GnomAD database, including 21,525 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 (21525 hom., cov: 32)
• Consequence: WDR27 NM_182552.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 3 publications found

Genes affected

WDR27 (HGNC:21248): (WD repeat domain 27) This gene encodes a protein with multiple WD repeats. Proteins with these repeats may form scaffolds for protein-protein interaction and play key roles in cell signalling. Alternative splicing results in multiple transcript variants, but the full-length structure of some of these variants cannot be determined. [provided by RefSeq, Nov 2015]

ENSG00000285733 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR27	NM_182552.5	c.2523+3776G>A		intron_variant	Intron 24 of 25	ENST00000448612.6	NP_872358.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR27	ENST00000448612.6	c.2523+3776G>A		intron_variant	Intron 24 of 25	1	NM_182552.5	ENSP00000416289.1
ENSG00000285733	ENST00000648086.1	c.533+3776G>A		intron_variant	Intron 5 of 7			ENSP00000497979.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73414 AN: 151922 Hom.: 21530 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.483 AC: 73414 AN: 152040 Hom.: 21525 Cov.: 32 AF XY: 0.479 AC XY: 35622 AN XY: 74292

African (AFR) AF: 0.194 AC: 8027 AN: 41466

American (AMR) AF: 0.397 AC: 6069 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3472

East Asian (EAS) AF: 0.138 AC: 711 AN: 5168

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4818

European-Finnish (FIN) AF: 0.684 AC: 7212 AN: 10550

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45303 AN: 67972

Other (OTH) AF: 0.492 AC: 1039 AN: 2112

Alfa AF: 0.534 Hom.: 4318

Bravo AF: 0.448

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.38
DANN	Benign	0.37
PhyloP100		-1.5
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: rs9295009; hg19: chr6-169979156;