6-169537865-G-A

Variant names:

• chr6-169537865-G-A
• rs1001844
• NM_182552.5:c.2645+34554C>T

Variant summary

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

The NM_182552.5(WDR27):​c.2645+34554C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,116 control chromosomes in the GnomAD database, including 1,946 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 0.11 (1946 hom., cov: 32)
• Consequence: WDR27 NM_182552.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 4 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	NM_182552.5	MANE Select	c.2645+34554C>T		intron	N/A	NP_872358.4
	WDR27	NM_001202550.2		c.2142+44971C>T		intron	N/A	NP_001189479.1
	WDR27	NM_001350623.2		c.1950+44971C>T		intron	N/A	NP_001337552.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	ENST00000448612.6	TSL:1 MANE Select	c.2645+34554C>T		intron	N/A	ENSP00000416289.1
	WDR27	ENST00000423258.5	TSL:1	c.2142+44971C>T		intron	N/A	ENSP00000397869.1
	ENSG00000285733	ENST00000648086.1		c.533+44971C>T		intron	N/A	ENSP00000497979.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16872 AN: 151998 Hom.: 1942 Cov.: 32

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.0647

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.111 AC: 16905 AN: 152116 Hom.: 1946 Cov.: 32 AF XY: 0.119 AC XY: 8831 AN XY: 74372

African (AFR) AF: 0.0811 AC: 3364 AN: 41460

American (AMR) AF: 0.255 AC: 3901 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3472

East Asian (EAS) AF: 0.585 AC: 3024 AN: 5170

South Asian (SAS) AF: 0.138 AC: 665 AN: 4820

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10584

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0648 AC: 4404 AN: 68014

Other (OTH) AF: 0.106 AC: 225 AN: 2114

Alfa AF: 0.0851 Hom.: 101

Bravo AF: 0.124

Asia WGS AF: 0.309 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-0.74
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: rs1001844; hg19: chr6-169937961;