Variant chr6-158767438-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001111077.2(EZR):c.1419A>C(p.Pro473=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0015 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

EZR
NM_001111077.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -8.03

Variant links:

Genes affected

EZR (HGNC:12691): (ezrin) The cytoplasmic peripheral membrane protein encoded by this gene functions as a protein-tyrosine kinase substrate in microvilli. As a member of the ERM protein family, this protein serves as an intermediate between the plasma membrane and the actin cytoskeleton. This protein plays a key role in cell surface structure adhesion, migration and organization, and it has been implicated in various human cancers. A pseudogene located on chromosome 3 has been identified for this gene. Alternatively spliced variants have also been described for this gene. [provided by RefSeq, Jul 2008]

EZR links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 6-158767438-T-G is Benign according to our data. Variant chr6-158767438-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 435106.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-8.03 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
EZR	NM_001111077.2 linkuse as main transcript	c.1419A>C	p.Pro473=	synonymous_variant	13/14	ENST00000367075.4	NP_001104547.1
EZR	NM_003379.5 linkuse as main transcript	c.1419A>C	p.Pro473=	synonymous_variant	12/13		NP_003370.2
EZR	XM_011536110.2 linkuse as main transcript	c.1011A>C	p.Pro337=	synonymous_variant	9/10		XP_011534412.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EZR	ENST00000367075.4 linkuse as main transcript	c.1419A>C	p.Pro473=	synonymous_variant	13/14	1	NM_001111077.2	ENSP00000356042	P1
EZR	ENST00000337147.11 linkuse as main transcript	c.1419A>C	p.Pro473=	synonymous_variant	12/13	1		ENSP00000338934	P1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

137854

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000273

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000145

Gnomad ASJ

AF:

0.000298

Gnomad EAS

AF:

0.000233

Gnomad SAS

AF:

0.000250

Gnomad FIN

AF:

0.000114

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000250

Gnomad OTH

AF:

0.000519

GnomAD3 exomes

AF:

0.00300

AC:

699

AN:

233284

Hom.:

AF XY:

0.00272

AC XY:

346

AN XY:

127058

show subpopulations

Gnomad AFR exome

AF:

0.00104

Gnomad AMR exome

AF:

0.00942

Gnomad ASJ exome

AF:

0.0102

Gnomad EAS exome

AF:

0.00174

Gnomad SAS exome

AF:

0.000205

Gnomad FIN exome

AF:

0.00286

Gnomad NFE exome

AF:

0.00189

Gnomad OTH exome

AF:

0.00471

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00145

AC:

1581

AN:

1090228

Hom.:

Cov.:

AF XY:

0.00153

AC XY:

838

AN XY:

546406

show subpopulations

Gnomad4 AFR exome

AF:

0.00295

Gnomad4 AMR exome

AF:

0.0138

Gnomad4 ASJ exome

AF:

0.00779

Gnomad4 EAS exome

AF:

0.000624

Gnomad4 SAS exome

AF:

0.000346

Gnomad4 FIN exome

AF:

0.00286

Gnomad4 NFE exome

AF:

0.000796

Gnomad4 OTH exome

AF:

0.00226

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000239

AC:

AN:

137952

Hom.:

Cov.:

AF XY:

0.000224

AC XY:

AN XY:

66866

show subpopulations

Gnomad4 AFR

AF:

0.000273

Gnomad4 AMR

AF:

0.000145

Gnomad4 ASJ

AF:

0.000298

Gnomad4 EAS

AF:

0.000233

Gnomad4 SAS

AF:

0.000250

Gnomad4 FIN

AF:

0.000114

Gnomad4 NFE

AF:

0.000250

Gnomad4 OTH

AF:

0.000514

Alfa

AF:

0.00107

Hom.:

Asia WGS

AF:

0.00289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jan 05, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

0.20

DANN

Benign

0.51

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