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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182552.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	NM_182552.5	MANE Select	c.2523+3776G>A		intron	N/A	NP_872358.4
	WDR27	NM_001202550.2		c.2142+3776G>A		intron	N/A	NP_001189479.1	A2RRH5-2
	WDR27	NM_001350623.2		c.1950+3776G>A		intron	N/A	NP_001337552.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	ENST00000448612.6	TSL:1 MANE Select	c.2523+3776G>A		intron	N/A	ENSP00000416289.1	A2RRH5-4
	WDR27	ENST00000423258.5	TSL:1	c.2142+3776G>A		intron	N/A	ENSP00000397869.1	A2RRH5-2
	ENSG00000285733	ENST00000648086.1		c.533+3776G>A		intron	N/A	ENSP00000497979.1	A0A3B3ITY5

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 v4.9

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;