6-169558886-G-A

Variant names:

• chr6-169558886-G-A
• rs3734905
• ENST00000546525.5:n.2946C>T

Variant summary

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

The ENST00000546525.5(WDR27):​n.2946C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 152,254 control chromosomes in the GnomAD database, including 893 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 0.091 (893 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDR27 ENST00000546525.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 16 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR27	NM_182552.5	c.2645+13533C>T		intron_variant	Intron 25 of 25	ENST00000448612.6	NP_872358.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR27	ENST00000448612.6	c.2645+13533C>T		intron_variant	Intron 25 of 25	1	NM_182552.5	ENSP00000416289.1
ENSG00000285733	ENST00000648086.1	c.533+23950C>T		intron_variant	Intron 5 of 7			ENSP00000497979.1

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13855 AN: 152136 Hom.: 892 Cov.: 32

Gnomad AFR AF: 0.0644

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0577

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0719

Gnomad OTH AF: 0.102

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0911 AC: 13872 AN: 152254 Hom.: 893 Cov.: 32 AF XY: 0.0965 AC XY: 7182 AN XY: 74442

African (AFR) AF: 0.0643 AC: 2672 AN: 41546

American (AMR) AF: 0.151 AC: 2308 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0577 AC: 200 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1103 AN: 5180

South Asian (SAS) AF: 0.276 AC: 1332 AN: 4820

European-Finnish (FIN) AF: 0.103 AC: 1094 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0719 AC: 4887 AN: 68016

Other (OTH) AF: 0.107 AC: 226 AN: 2112

Alfa AF: 0.0837 Hom.: 2241

Bravo AF: 0.0933

Asia WGS AF: 0.290 AC: 1007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3734905; hg19: chr6-169958982;