6-169453201-C-T

Variant names:

• chr6-169453201-C-T
• rs911839
• ENST00000648086.1:c.534-19799G>A

Variant summary

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

The ENST00000648086.1(ENSG00000285733):​c.534-19799G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,084 control chromosomes in the GnomAD database, including 26,316 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 0.56 (26316 hom., cov: 33)
• Consequence: ENSG00000285733 ENST00000648086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.982
• Publications: 9 publications found

Genes affected

ENSG00000285733 (HGNC:):

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000648086.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285733	ENST00000648086.1		c.534-19799G>A		intron	N/A	ENSP00000497979.1	A0A3B3ITY5
	ENSG00000285733	ENST00000649579.1		n.*1001+4333G>A		intron	N/A	ENSP00000497123.1	A0A3B3IS69
	ENSG00000285733	ENST00000650382.1		n.973+4333G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84499 AN: 151966 Hom.: 26257 Cov.: 33

Gnomad AFR AF: 0.789

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.556 AC: 84621 AN: 152084 Hom.: 26316 Cov.: 33 AF XY: 0.562 AC XY: 41739 AN XY: 74328

African (AFR) AF: 0.790 AC: 32757 AN: 41490

American (AMR) AF: 0.629 AC: 9627 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1477 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4714 AN: 5178

South Asian (SAS) AF: 0.658 AC: 3172 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4050 AN: 10538

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27180 AN: 67982

Other (OTH) AF: 0.532 AC: 1122 AN: 2110

Alfa AF: 0.434 Hom.: 16659

Bravo AF: 0.584

Asia WGS AF: 0.791 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.33
PhyloP100		-0.98

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs911839;

hg19: chr6-169853296;