6-158767438-T-G

Variant summary

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

The NM_001111077.2(EZR):ā€‹c.1419A>Cā€‹(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 (ā˜…).

Frequency

Genomes: š‘“ 0.00024 ( 0 hom., cov: 31)
Exomes š‘“: 0.0015 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

EZR
NM_001111077.2 synonymous

Scores

2

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]

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 UniProt
EZRNM_001111077.2 linkuse as main transcriptc.1419A>C p.Pro473= synonymous_variant 13/14 ENST00000367075.4 NP_001104547.1
EZRNM_003379.5 linkuse as main transcriptc.1419A>C p.Pro473= synonymous_variant 12/13 NP_003370.2
EZRXM_011536110.2 linkuse as main transcriptc.1011A>C p.Pro337= synonymous_variant 9/10 XP_011534412.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EZRENST00000367075.4 linkuse as main transcriptc.1419A>C p.Pro473= synonymous_variant 13/141 NM_001111077.2 ENSP00000356042 P1
EZRENST00000337147.11 linkuse as main transcriptc.1419A>C p.Pro473= synonymous_variant 12/131 ENSP00000338934 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
33
AN:
137854
Hom.:
0
Cov.:
31
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.:
0
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.:
0
Cov.:
38
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:
33
AN:
137952
Hom.:
0
Cov.:
31
AF XY:
0.000224
AC XY:
15
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.:
0
Asia WGS
AF:
0.00289
AC:
10
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 submitterclinical testingGenetic Services Laboratory, University of ChicagoJan 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.

Other links and lift over

dbSNP: rs776473073; hg19: chr6-159188470; API