Variant 7-5214596-C-G 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.273C>G(p.Val91Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.985 in 1,614,266 control chromosomes in the GnomAD database, including 783,517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.99 ( 74235 hom., cov: 34)

Exomes 𝑓: 0.99 ( 709282 hom. )

Consequence

WIPI2
NM_015610.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.27

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:

WIPI2 (HGNC:):

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=-0.75).

BP6

Variant 7-5214596-C-G is Benign according to our data. Variant chr7-5214596-C-G is described in ClinVar as [Benign]. Clinvar id is 3059558.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-3.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WIPI2	NM_015610.4 linkuse as main transcript	c.273C>G	p.Val91Val	synonymous_variant	4/13	ENST00000288828.9	NP_056425.1	Q9Y4P8-1A0A024R823

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WIPI2	ENST00000288828.9 linkuse as main transcript	c.273C>G	p.Val91Val	synonymous_variant	4/13	1	NM_015610.4	ENSP00000288828.4		Q9Y4P8-1

Frequencies

GnomAD3 genomes

AF:

0.987

AC:

150281

AN:

152256

Hom.:

74176

Cov.:

show subpopulations

Gnomad AFR

AF:

0.997

Gnomad AMI

AF:

0.999

Gnomad AMR

AF:

0.992

Gnomad ASJ

AF:

0.996

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.996

Gnomad FIN

AF:

0.970

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

0.980

Gnomad OTH

AF:

0.994

GnomAD3 exomes

AF:

0.987

AC:

248255

AN:

251494

Hom.:

122539

AF XY:

0.987

AC XY:

134132

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.998

Gnomad AMR exome

AF:

0.994

Gnomad ASJ exome

AF:

0.999

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.994

Gnomad FIN exome

AF:

0.970

Gnomad NFE exome

AF:

0.982

Gnomad OTH exome

AF:

0.985

GnomAD4 exome

AF:

0.985

AC:

1440031

AN:

1461892

Hom.:

709282

Cov.:

AF XY:

0.985

AC XY:

716397

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.998

Gnomad4 AMR exome

AF:

0.994

Gnomad4 ASJ exome

AF:

0.997

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.995

Gnomad4 FIN exome

AF:

0.968

Gnomad4 NFE exome

AF:

0.983

Gnomad4 OTH exome

AF:

0.987

GnomAD4 genome

AF:

0.987

AC:

150399

AN:

152374

Hom.:

74235

Cov.:

AF XY:

0.987

AC XY:

73546

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.997

Gnomad4 AMR

AF:

0.992

Gnomad4 ASJ

AF:

0.996

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.996

Gnomad4 FIN

AF:

0.970

Gnomad4 NFE

AF:

0.980

Gnomad4 OTH

AF:

0.994

Alfa

AF:

0.983

Hom.:

23849

Bravo

AF:

0.990

Asia WGS

AF:

0.999

AC:

3472

AN:

3478

EpiCase

AF:

0.983

EpiControl

AF:

0.987

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

Nov 05, 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

-0.75

CADD

Benign

0.48

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

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

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