chr6-169572543-C-CAAA

Variant names:

• chr6-169572543-C-CAAA
• rs376783967
• NM_182552.5:c.2524-6_2524-4dupTTT

Variant summary

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

The NM_182552.5(WDR27):​c.2524-6_2524-4dupTTT 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 0.019 (103 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.2524-6_2524-4dupTTT		splice_region intron	N/A	NP_872358.4
	WDR27	NM_001202550.2		c.2142+10290_2142+10292dupTTT		intron	N/A	NP_001189479.1	A2RRH5-2
	WDR27	NM_001350623.2		c.1950+10290_1950+10292dupTTT		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_2524-3insTTT		splice_region intron	N/A	ENSP00000416289.1	A2RRH5-4
	WDR27	ENST00000423258.5	TSL:1	c.2142+10292_2142+10293insTTT		intron	N/A	ENSP00000397869.1	A2RRH5-2
	ENSG00000285733	ENST00000648086.1		c.533+10292_533+10293insTTT		intron	N/A	ENSP00000497979.1	A0A3B3ITY5

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 1743 AN: 92248 Hom.: 103 Cov.: 0

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0694

Gnomad ASJ AF: 0.00901

Gnomad EAS AF: 0.0222

Gnomad SAS AF: 0.0142

Gnomad FIN AF: 0.00819

Gnomad MID AF: 0.0149

Gnomad NFE AF: 0.0151

Gnomad OTH AF: 0.0291

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: 0.0189 AC: 1746 AN: 92234 Hom.: 103 Cov.: 0 AF XY: 0.0183 AC XY: 779 AN XY: 42662

African (AFR) AF: 0.0117 AC: 203 AN: 17284

American (AMR) AF: 0.0695 AC: 555 AN: 7988

Ashkenazi Jewish (ASJ) AF: 0.00901 AC: 25 AN: 2776

East Asian (EAS) AF: 0.0222 AC: 48 AN: 2158

South Asian (SAS) AF: 0.0143 AC: 37 AN: 2584

European-Finnish (FIN) AF: 0.00819 AC: 36 AN: 4396

Middle Eastern (MID) AF: 0.0160 AC: 3 AN: 188

European-Non Finnish (NFE) AF: 0.0151 AC: 800 AN: 52876

Other (OTH) AF: 0.0306 AC: 39 AN: 1276

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

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;