Variant rs17380141 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_020335.3(VANGL2):c.1401G>A(p.Pro467Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 1,613,824 control chromosomes in the GnomAD database, including 63,777 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5345 hom., cov: 31)

Exomes 𝑓: 0.28 ( 58432 hom. )

Consequence

VANGL2
NM_020335.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.189

Variant links:

Genes affected

VANGL2 (HGNC:15511): (VANGL planar cell polarity protein 2) The protein encoded by this gene is a membrane protein involved in the regulation of planar cell polarity, especially in the stereociliary bundles of the cochlea. The encoded protein transmits directional signals to individual cells or groups of cells in epithelial sheets. This protein is also involved in the development of the neural plate. [provided by RefSeq, Sep 2011]

VANGL2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP7

Synonymous conserved (PhyloP=-0.189 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
VANGL2	NM_020335.3 linkuse as main transcript	c.1401G>A	p.Pro467Pro	synonymous_variant	8/8	ENST00000368061.3	NP_065068.1	Q9ULK5A8K4L6
VANGL2	XM_005245357.2 linkuse as main transcript	c.1401G>A	p.Pro467Pro	synonymous_variant	9/9		XP_005245414.1	Q9ULK5
VANGL2	XM_011509804.2 linkuse as main transcript	c.1401G>A	p.Pro467Pro	synonymous_variant	8/8		XP_011508106.1	Q9ULK5
VANGL2	XM_047426020.1 linkuse as main transcript	c.1401G>A	p.Pro467Pro	synonymous_variant	8/8		XP_047281976.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
VANGL2	ENST00000368061.3 linkuse as main transcript	c.1401G>A	p.Pro467Pro	synonymous_variant	8/8	2	NM_020335.3	ENSP00000357040.2		Q9ULK5
VANGL2	ENST00000696602.1 linkuse as main transcript	c.1545G>A	p.Pro515Pro	synonymous_variant	8/8			ENSP00000512747.1		A0A8Q3SIN7

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39248

AN:

151848

Hom.:

5345

Cov.:

show subpopulations

Gnomad AFR

AF:

0.229

Gnomad AMI

AF:

0.424

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.0969

Gnomad SAS

AF:

0.300

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.320

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.277

GnomAD3 exomes

AF:

0.253

AC:

63698

AN:

251294

Hom.:

8490

AF XY:

0.261

AC XY:

35414

AN XY:

135812

show subpopulations

Gnomad AFR exome

AF:

0.233

Gnomad AMR exome

AF:

0.206

Gnomad ASJ exome

AF:

0.263

Gnomad EAS exome

AF:

0.100

Gnomad SAS exome

AF:

0.294

Gnomad FIN exome

AF:

0.227

Gnomad NFE exome

AF:

0.288

Gnomad OTH exome

AF:

0.264

GnomAD4 exome

AF:

0.280

AC:

408893

AN:

1461858

Hom.:

58432

Cov.:

AF XY:

0.280

AC XY:

203920

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.231

Gnomad4 AMR exome

AF:

0.213

Gnomad4 ASJ exome

AF:

0.256

Gnomad4 EAS exome

AF:

0.0848

Gnomad4 SAS exome

AF:

0.293

Gnomad4 FIN exome

AF:

0.229

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.258

AC:

39266

AN:

151966

Hom.:

5345

Cov.:

AF XY:

0.256

AC XY:

19014

AN XY:

74270

show subpopulations

Gnomad4 AFR

AF:

0.229

Gnomad4 AMR

AF:

0.250

Gnomad4 ASJ

AF:

0.260

Gnomad4 EAS

AF:

0.0972

Gnomad4 SAS

AF:

0.299

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.289

Gnomad4 OTH

AF:

0.276

Alfa

AF:

0.273

Hom.:

3027

Bravo

AF:

0.261

Asia WGS

AF:

0.199

AC:

692

AN:

3478

EpiCase

AF:

0.304

EpiControl

AF:

0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.8

DANN

Benign

0.69

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over