chr6-169453201-C-T

Position:

• chr6-169453201-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR27	XM_011535687.4	c.2524-22489G>A		intron_variant			XP_011533989.1
WDR27	XM_011535688.4	c.2524-22489G>A		intron_variant			XP_011533990.1
WDR27	XR_007059231.1	n.3192-22489G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285733	ENST00000648086.1	c.534-19799G>A		intron_variant				ENSP00000497979.1
ENSG00000285733	ENST00000649579.1	n.*1001+4333G>A		intron_variant				ENSP00000497123.1
ENSG00000285733	ENST00000650382.1	n.973+4333G>A		intron_variant

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

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.532

Alfa AF: 0.425 Hom.: 13169

Bravo AF: 0.584

Asia WGS AF: 0.791 AC: 2748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs911839; hg19: chr6-169853296;