6-169572543-CAAAAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAA

Variant names:

• chr6-169572543-C-CAA
• rs376783967
• NM_182552.5:c.2524-5_2524-4dupTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_182552.5(WDR27):​c.2524-5_2524-4dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.070 (926 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: Uncertain_significance. The variant received 0 ACMG points.

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.2524-5_2524-4dupTT		splice_region intron	N/A	NP_872358.4
	WDR27	NM_001202550.2		c.2142+10291_2142+10292dupTT		intron	N/A	NP_001189479.1	A2RRH5-2
	WDR27	NM_001350623.2		c.1950+10291_1950+10292dupTT		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_2524-3insTT		splice_region intron	N/A	ENSP00000416289.1	A2RRH5-4
	WDR27	ENST00000423258.5	TSL:1	c.2142+10292_2142+10293insTT		intron	N/A	ENSP00000397869.1	A2RRH5-2
	ENSG00000285733	ENST00000648086.1		c.533+10292_533+10293insTT		intron	N/A	ENSP00000497979.1	A0A3B3ITY5

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 6480 AN: 92096 Hom.: 925 Cov.: 0

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.0440

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.0651

Gnomad FIN AF: 0.0171

Gnomad MID AF: 0.0245

Gnomad NFE AF: 0.0316

Gnomad OTH AF: 0.0688

GnomAD2 exomes AF: 0.00 AC: 0 AN: 10 AF XY: 0.00

Gnomad NFE exome AF: 0.00

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 Data not reliable, filtered out with message: AS_VQSR AF: 0.0704 AC: 6484 AN: 92078 Hom.: 926 Cov.: 0 AF XY: 0.0703 AC XY: 2994 AN XY: 42602

African (AFR) AF: 0.149 AC: 2575 AN: 17240

American (AMR) AF: 0.0836 AC: 668 AN: 7986

Ashkenazi Jewish (ASJ) AF: 0.0440 AC: 122 AN: 2772

East Asian (EAS) AF: 0.520 AC: 1111 AN: 2138

South Asian (SAS) AF: 0.0653 AC: 168 AN: 2574

European-Finnish (FIN) AF: 0.0171 AC: 75 AN: 4386

Middle Eastern (MID) AF: 0.0266 AC: 5 AN: 188

European-Non Finnish (NFE) AF: 0.0316 AC: 1667 AN: 52816

Other (OTH) AF: 0.0677 AC: 86 AN: 1270

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

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

Other links and lift over

dbSNP: rs376783967; hg19: chr6-169972639;