Genetic Variant WDR27:c.2524-7_2524-4delTTTT (chr6-169572543-CAAAA-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_182552.5(WDR27):c.2524-7_2524-4delTTTT 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. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.54 ( 12667 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

Benign criteria provided, single submitter B:1

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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_182552.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 6-169572543-CAAAA-C is Benign according to our data. Variant chr6-169572543-CAAAA-C is described in ClinVar as Benign. ClinVar VariationId is 2808640.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 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.2524-7_2524-4delTTTT	splice_region intron	N/A	NP_872358.4
WDR27	NM_001202550.2		c.2142+10289_2142+10292delTTTT	intron	N/A	NP_001189479.1	A2RRH5-2
WDR27	NM_001350623.2		c.1950+10289_1950+10292delTTTT	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.2524-7_2524-4delTTTT	splice_region intron	N/A	ENSP00000416289.1	A2RRH5-4
WDR27	ENST00000423258.5	TSL:1	c.2142+10289_2142+10292delTTTT	intron	N/A	ENSP00000397869.1	A2RRH5-2
ENSG00000285733	ENST00000648086.1		c.533+10289_533+10292delTTTT	intron	N/A	ENSP00000497979.1	A0A3B3ITY5

Frequencies

GnomAD3 genomes

AF:

0.543

AC:

49865

AN:

91912

Hom.:

12675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.502

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.0290

Gnomad SAS

AF:

0.472

Gnomad FIN

AF:

0.679

Gnomad MID

AF:

0.587

Gnomad NFE

AF:

0.646

Gnomad OTH

AF:

0.535

GnomAD2 exomes

AF:

0.00

AC:

AN:

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:

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:

0.542

AC:

49837

AN:

91894

Hom.:

12667

Cov.:

AF XY:

0.537

AC XY:

22853

AN XY:

42562

show subpopulations

African (AFR)

AF:

0.269

AC:

4631

AN:

17188

American (AMR)

AF:

0.501

AC:

4013

AN:

8008

Ashkenazi Jewish (ASJ)

AF:

0.607

AC:

1679

AN:

2768

East Asian (EAS)

AF:

0.0286

AC:

AN:

2168

South Asian (SAS)

AF:

0.472

AC:

1211

AN:

2566

European-Finnish (FIN)

AF:

0.679

AC:

2987

AN:

4396

Middle Eastern (MID)

AF:

0.583

AC:

112

AN:

192

European-Non Finnish (NFE)

AF:

0.646

AC:

34027

AN:

52636

Other (OTH)

AF:

0.531

AC:

673

AN:

1268

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

756

1512

2268

3024

3780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.35

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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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6-169572543-CAAAAAAAAAAAAAAA-CAAAAAAAAAAA

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