Variant chr6-169572531-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_182552.5(WDR27):c.2533C>T(p.Arg845Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 18965 hom., cov: 19)

Exomes 𝑓: 0.34 ( 6 hom. )

Failed GnomAD Quality Control

Consequence

WDR27
NM_182552.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.22

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0020298362).

BP6

Variant 6-169572531-G-A is Benign according to our data. Variant chr6-169572531-G-A is described in ClinVar as [Benign]. Clinvar id is 768123.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WDR27	NM_182552.5 linkuse as main transcript	c.2533C>T	p.Arg845Cys	missense_variant	25/26	ENST00000448612.6	NP_872358.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WDR27	ENST00000448612.6 linkuse as main transcript	c.2533C>T	p.Arg845Cys	missense_variant	25/26	1	NM_182552.5	ENSP00000416289	A2	A2RRH5-4

Frequencies

GnomAD3 genomes

AF:

0.513

AC:

65993

AN:

128752

Hom.:

18971

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.688

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.610

Gnomad EAS

AF:

0.0214

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.702

Gnomad MID

AF:

0.624

Gnomad NFE

AF:

0.654

Gnomad OTH

AF:

0.518

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.338

AC:

AN:

Hom.:

Cov.:

AF XY:

0.344

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.397

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.512

AC:

65987

AN:

128760

Hom.:

18965

Cov.:

AF XY:

0.507

AC XY:

30980

AN XY:

61078

show subpopulations

Gnomad4 AFR

AF:

0.252

Gnomad4 AMR

AF:

0.473

Gnomad4 ASJ

AF:

0.610

Gnomad4 EAS

AF:

0.0212

Gnomad4 SAS

AF:

0.384

Gnomad4 FIN

AF:

0.702

Gnomad4 NFE

AF:

0.654

Gnomad4 OTH

AF:

0.514

Alfa

AF:

0.548

Hom.:

2744

Bravo

AF:

0.442

TwinsUK

AF:

0.667

AC:

2475

ALSPAC

AF:

0.638

AC:

2460

ExAC

AF:

0.237

AC:

328

Asia WGS

AF:

0.161

AC:

552

AN:

3422

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 07, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.78

CADD

Benign

1.7

DANN

Benign

0.68

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.0011

LIST_S2

Benign

0.14

MetaRNN

Benign

0.0020

MetaSVM

Benign

-0.96

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.87

REVEL

Benign

0.064

Sift

Benign

0.053

Sift4G

Benign

0.11

Vest4

0.024

MPC

0.053

ClinPred

0.074

GERP RS

-0.99

gMVP

0.22

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over