Genetic Variant NM_182552.5:c.2524-9_2524-4delTTTTTT (chr6-169572543-CAAAAAA-C) – ACMG Classification: Benign (-8 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.347

Publications

0 publications found

Variant links:

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]

WDR27 links:

ENSG00000285733 (HGNC:):

ENSG00000285733 links:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	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

Gene	Transcript	Tags	HGVSc	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.:

Cov.:

show subpopulations

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:

AN:

AF XY:

0.167

show subpopulations

Gnomad NFE exome

AF:

0.100

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0305

AC:

2814

AN:

92268

Hom.:

Cov.:

AF XY:

0.0329

AC XY:

1405

AN XY:

42690

show subpopulations

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:

AN:

186

European-Non Finnish (NFE)

AF:

0.0241

AC:

1275

AN:

52858

Other (OTH)

AF:

0.0321

AC:

AN:

1276

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

191

286

382

477

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

152

190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.35

Mutation Taster

=90/10

polymorphism

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over