Variant chr7-5217942-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_015610.4(WIPI2):c.597G>A(p.Pro199=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,613,952 control chromosomes in the GnomAD database, including 11,186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.082 ( 707 hom., cov: 33)

Exomes 𝑓: 0.11 ( 10479 hom. )

Consequence

WIPI2
NM_015610.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.28

Variant links:

Genes affected

WIPI2 (HGNC:32225): (WD repeat domain, phosphoinositide interacting 2) WD40 repeat proteins are key components of many essential biologic functions. They regulate the assembly of multiprotein complexes by presenting a beta-propeller platform for simultaneous and reversible protein-protein interactions. Members of the WIPI subfamily of WD40 repeat proteins, such as WIPI2, have a 7-bladed propeller structure and contain a conserved motif for interaction with phospholipids (Proikas-Cezanne et al., 2004 [PubMed 15602573]).[supplied by OMIM, Mar 2008]

WIPI2 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 (BayesDel_noAF=-0.7).

BP6

Variant 7-5217942-G-A is Benign according to our data. Variant chr7-5217942-G-A is described in ClinVar as [Benign]. Clinvar id is 3059569.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-1.28 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WIPI2	NM_015610.4 linkuse as main transcript	c.597G>A	p.Pro199=	synonymous_variant	7/13	ENST00000288828.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WIPI2	ENST00000288828.9 linkuse as main transcript	c.597G>A	p.Pro199=	synonymous_variant	7/13	1	NM_015610.4		Q9Y4P8-1

Frequencies

GnomAD3 genomes

AF:

0.0818

AC:

12456

AN:

152184

Hom.:

706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0234

Gnomad AMI

AF:

0.234

Gnomad AMR

AF:

0.100

Gnomad ASJ

AF:

0.170

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0542

Gnomad FIN

AF:

0.0307

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.105

GnomAD3 exomes

AF:

0.0851

AC:

21391

AN:

251430

Hom.:

1280

AF XY:

0.0879

AC XY:

11943

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.0215

Gnomad AMR exome

AF:

0.0640

Gnomad ASJ exome

AF:

0.161

Gnomad EAS exome

AF:

0.000598

Gnomad SAS exome

AF:

0.0644

Gnomad FIN exome

AF:

0.0330

Gnomad NFE exome

AF:

0.122

Gnomad OTH exome

AF:

0.101

GnomAD4 exome

AF:

0.113

AC:

165021

AN:

1461650

Hom.:

10479

Cov.:

AF XY:

0.112

AC XY:

81525

AN XY:

727116

show subpopulations

Gnomad4 AFR exome

AF:

0.0205

Gnomad4 AMR exome

AF:

0.0680

Gnomad4 ASJ exome

AF:

0.160

Gnomad4 EAS exome

AF:

0.000378

Gnomad4 SAS exome

AF:

0.0644

Gnomad4 FIN exome

AF:

0.0354

Gnomad4 NFE exome

AF:

0.128

Gnomad4 OTH exome

AF:

0.112

GnomAD4 genome

AF:

0.0818

AC:

12458

AN:

152302

Hom.:

707

Cov.:

AF XY:

0.0791

AC XY:

5889

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.0234

Gnomad4 AMR

AF:

0.100

Gnomad4 ASJ

AF:

0.170

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.0546

Gnomad4 FIN

AF:

0.0307

Gnomad4 NFE

AF:

0.122

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.112

Hom.:

833

Bravo

AF:

0.0869

Asia WGS

AF:

0.0300

AC:

106

AN:

3478

EpiCase

AF:

0.130

EpiControl

AF:

0.130

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

WIPI2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 03, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

3.9

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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