14-64167266-G-A

Position:

chr14-64167266-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000555002.6(SYNE2):c.16639G>A(p.Asp5547Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0137 in 1,614,194 control chromosomes in the GnomAD database, including 225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D5547G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.010 ( 13 hom., cov: 32)

Exomes 𝑓: 0.014 ( 212 hom. )

Consequence

SYNE2
ENST00000555002.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 4.65

Variant links:

Genes affected

SYNE2 (HGNC:17084): (spectrin repeat containing nuclear envelope protein 2) The protein encoded by this gene is a nuclear outer membrane protein that binds cytoplasmic F-actin. This binding tethers the nucleus to the cytoskeleton and aids in the maintenance of the structural integrity of the nucleus. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

SYNE2 links:

ESR2 (HGNC:3468): (estrogen receptor 2) This gene encodes a member of the family of estrogen receptors and superfamily of nuclear receptor transcription factors. The gene product contains an N-terminal DNA binding domain and C-terminal ligand binding domain and is localized to the nucleus, cytoplasm, and mitochondria. Upon binding to 17beta-estradiol or related ligands, the encoded protein forms homo- or hetero-dimers that interact with specific DNA sequences to activate transcription. Some isoforms dominantly inhibit the activity of other estrogen receptor family members. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been fully characterized. [provided by RefSeq, Jul 2008]

ESR2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024761856).

BP6

Variant 14-64167266-G-A is Benign according to our data. Variant chr14-64167266-G-A is described in ClinVar as [Benign]. Clinvar id is 313627.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-64167266-G-A is described in Lovd as [Benign]. Variant chr14-64167266-G-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0105 (1594/152318) while in subpopulation SAS AF= 0.0228 (110/4824). AF 95% confidence interval is 0.0193. There are 13 homozygotes in gnomad4. There are 713 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1594 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNE2	NM_182914.3 linkuse as main transcript	c.16639G>A	p.Asp5547Asn	missense_variant	91/116	ENST00000555002.6	NP_878918.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNE2	ENST00000555002.6 linkuse as main transcript	c.16639G>A	p.Asp5547Asn	missense_variant	91/116	1	NM_182914.3	ENSP00000450831	P4	Q8WXH0-2

Frequencies

GnomAD3 genomes

AF:

0.0105

AC:

1593

AN:

152200

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00384

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.00759

Gnomad ASJ

AF:

0.0449

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0228

Gnomad FIN

AF:

0.00348

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0141

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.0132

AC:

3312

AN:

251298

Hom.:

AF XY:

0.0143

AC XY:

1947

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.00345

Gnomad AMR exome

AF:

0.00616

Gnomad ASJ exome

AF:

0.0457

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0243

Gnomad FIN exome

AF:

0.00291

Gnomad NFE exome

AF:

0.0149

Gnomad OTH exome

AF:

0.0135

GnomAD4 exome

AF:

0.0140

AC:

20453

AN:

1461876

Hom.:

212

Cov.:

AF XY:

0.0145

AC XY:

10536

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00236

Gnomad4 AMR exome

AF:

0.00642

Gnomad4 ASJ exome

AF:

0.0460

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0255

Gnomad4 FIN exome

AF:

0.00328

Gnomad4 NFE exome

AF:

0.0140

Gnomad4 OTH exome

AF:

0.0144

GnomAD4 genome

AF:

0.0105

AC:

1594

AN:

152318

Hom.:

Cov.:

AF XY:

0.00957

AC XY:

713

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00385

Gnomad4 AMR

AF:

0.00758

Gnomad4 ASJ

AF:

0.0449

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0228

Gnomad4 FIN

AF:

0.00348

Gnomad4 NFE

AF:

0.0141

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.0157

Hom.:

Bravo

AF:

0.0105

TwinsUK

AF:

0.0132

AC:

ALSPAC

AF:

0.0130

AC:

ESP6500AA

AF:

0.00386

AC:

ESP6500EA

AF:

0.0149

AC:

128

ExAC

AF:

0.0132

AC:

1597

Asia WGS

AF:

0.00635

AC:

AN:

3478

EpiCase

AF:

0.0176

EpiControl

AF:

0.0160

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Mar 19, 2020	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

Emery-Dreifuss muscular dystrophy 5, autosomal dominant

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 12, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.075

.;T;T;T;T

Eigen

Benign

0.17

Eigen_PC

Uncertain

0.23

FATHMM_MKL

Uncertain

0.87

LIST_S2

Benign

0.78

T;T;T;T;T

MetaRNN

Benign

0.0025

T;T;T;T;T

MetaSVM

Benign

-0.87

MutationAssessor

Uncertain

2.4

M;.;M;.;.

MutationTaster

Benign

1.0

D;N;N;N;N;N;N

PrimateAI

Benign

0.27

PROVEAN

Uncertain

-4.2

D;.;D;D;D

REVEL

Benign

0.16

Sift

Uncertain

0.0030

D;.;D;D;D

Sift4G

Uncertain

0.0070

D;D;D;D;D

Polyphen

0.78

P;.;P;B;.

Vest4

0.13

MPC

0.050

ClinPred

0.052

GERP RS

4.9

Varity_R

0.30

gMVP

0.24

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