6-169572543-CAAAAAAAAAAAAAAA-CAAAAAAAAAAAAAAAA

Variant names:

• chr6-169572543-C-CA
• rs376783967
• NM_182552.5:c.2524-4dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_182552.5(WDR27):​c.2524-4dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.057 (436 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: WDR27 NM_182552.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 0 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0857 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	NM_182552.5	MANE Select	c.2524-4dupT		splice_region intron	N/A	NP_872358.4
	WDR27	NM_001202550.2		c.2142+10292dupT		intron	N/A	NP_001189479.1	A2RRH5-2
	WDR27	NM_001350623.2		c.1950+10292dupT		intron	N/A	NP_001337552.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WDR27	ENST00000448612.6	TSL:1 MANE Select	c.2524-4_2524-3insT		splice_region intron	N/A	ENSP00000416289.1	A2RRH5-4
	WDR27	ENST00000423258.5	TSL:1	c.2142+10292_2142+10293insT		intron	N/A	ENSP00000397869.1	A2RRH5-2
	ENSG00000285733	ENST00000648086.1		c.533+10292_533+10293insT		intron	N/A	ENSP00000497979.1	A0A3B3ITY5

Frequencies

GnomAD3 genomes AF: 0.0569 AC: 5242 AN: 92174 Hom.: 438 Cov.: 0

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.0895

Gnomad AMR AF: 0.0382

Gnomad ASJ AF: 0.0425

Gnomad EAS AF: 0.0685

Gnomad SAS AF: 0.0407

Gnomad FIN AF: 0.0118

Gnomad MID AF: 0.0545

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0465

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 28 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 28

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0568 AC: 5235 AN: 92156 Hom.: 436 Cov.: 0 AF XY: 0.0567 AC XY: 2418 AN XY: 42636

African (AFR) AF: 0.0894 AC: 1543 AN: 17266

American (AMR) AF: 0.0382 AC: 306 AN: 8012

Ashkenazi Jewish (ASJ) AF: 0.0425 AC: 118 AN: 2776

East Asian (EAS) AF: 0.0676 AC: 146 AN: 2160

South Asian (SAS) AF: 0.0391 AC: 101 AN: 2580

European-Finnish (FIN) AF: 0.0118 AC: 52 AN: 4392

Middle Eastern (MID) AF: 0.0538 AC: 10 AN: 186

European-Non Finnish (NFE) AF: 0.0537 AC: 2836 AN: 52806

Other (OTH) AF: 0.0471 AC: 60 AN: 1274

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.35
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs376783967; hg19: chr6-169972639;