Genetic Variant WDR27:c.2524-9_2524-4delTTTTTT (chr6-169572543-CAAAAAA-C) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

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 Lovd as Benign (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

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 made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 6-169572543-CAAAAAA-C is Benign according to our data. Variant chr6-169572543-CAAAAAA-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WDR27	NM_182552.5 link	c.2524-9_2524-4delTTTTTT		splice_region_variant, intron_variant	Intron 24 of 25	ENST00000448612.6	NP_872358.4	A2RRH5-4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WDR27	ENST00000448612.6 link	c.2524-9_2524-4delTTTTTT		splice_region_variant, intron_variant	Intron 24 of 25	1	NM_182552.5	ENSP00000416289.1		A2RRH5-4
ENSG00000285733	ENST00000648086.1 link	c.533+10287_533+10292delTTTTTT		intron_variant	Intron 5 of 7			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

GnomAD3 exomes

AF:

0.100

AC:

AN:

Hom.:

AF XY:

0.167

AC XY:

AN XY:

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:

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.0305

AC:

2814

AN:

92268

Hom.:

Cov.:

AF XY:

0.0329

AC XY:

1405

AN XY:

42690

show subpopulations

Gnomad4 AFR

AF:

0.0296

Gnomad4 AMR

AF:

0.0212

Gnomad4 ASJ

AF:

0.0573

Gnomad4 EAS

AF:

0.144

Gnomad4 SAS

AF:

0.0596

Gnomad4 FIN

AF:

0.0414

Gnomad4 NFE

AF:

0.0241

Gnomad4 OTH

AF:

0.0321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

6-169572543-CAAAAAAAAAAAAAAA-CAAAAAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over