6-169572543-CAAAAAAAAAAAAAAA-CAAAAAAAAA

Variant names:

• chr6-169572543-CAAAAAA-C
• rs376783967
• NM_182552.5:c.2524-9_2524-4delTTTTTT

Variant summary

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

The NM_182552.5(WDR27):​c.2524-9_2524-4delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as (no stars).

• Frequency:
  • Genomes: 𝑓 0.030 (40 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 (EAS) allele frequency at 95% confidence interval = 0.131 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.2524-9_2524-4delTTTTTT		splice_region intron	N/A	NP_872358.4
	WDR27	NM_001202550.2		c.2142+10287_2142+10292delTTTTTT		intron	N/A	NP_001189479.1	A2RRH5-2
	WDR27	NM_001350623.2		c.1950+10287_1950+10292delTTTTTT		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.2524-9_2524-4delTTTTTT		splice_region intron	N/A	ENSP00000416289.1	A2RRH5-4
	WDR27	ENST00000423258.5	TSL:1	c.2142+10287_2142+10292delTTTTTT		intron	N/A	ENSP00000397869.1	A2RRH5-2
	ENSG00000285733	ENST00000648086.1		c.533+10287_533+10292delTTTTTT		intron	N/A	ENSP00000497979.1	A0A3B3ITY5

Frequencies

GnomAD3 genomes AF: 0.0304 AC: 2809 AN: 92286 Hom.: 39 Cov.: 0

Gnomad AFR AF: 0.0296

Gnomad AMI AF: 0.00424

Gnomad AMR AF: 0.0212

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0347

Gnomad NFE AF: 0.0241

Gnomad OTH AF: 0.0291

GnomAD2 exomes AF: 0.100 AC: 1 AN: 10 AF XY: 0.167

Gnomad NFE exome AF: 0.100

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 28 Hom.: 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: 0.0305 AC: 2814 AN: 92268 Hom.: 40 Cov.: 0 AF XY: 0.0329 AC XY: 1405 AN XY: 42690

African (AFR) AF: 0.0296 AC: 512 AN: 17276

American (AMR) AF: 0.0212 AC: 170 AN: 8028

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 159 AN: 2776

East Asian (EAS) AF: 0.144 AC: 311 AN: 2158

South Asian (SAS) AF: 0.0596 AC: 154 AN: 2586

European-Finnish (FIN) AF: 0.0414 AC: 183 AN: 4416

Middle Eastern (MID) AF: 0.0323 AC: 6 AN: 186

European-Non Finnish (NFE) AF: 0.0241 AC: 1275 AN: 52858

Other (OTH) AF: 0.0321 AC: 41 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		=90/10	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;