rs1001844

chr6-169537865-G-Achr6-169537865-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WDR27	NM_182552.5	c.2645+34554C>T		intron_variant		ENST00000448612.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WDR27	ENST00000448612.6	c.2645+34554C>T		intron_variant		1	NM_182552.5	A2

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

Gnomad4 AFR AF: 0.0811

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.0441

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0853 Hom.: 100

Bravo AF: 0.124

Asia WGS AF: 0.309 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs1001844; hg19: chr6-169937961;