rs7161192

chr14-64170429-C-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_182914.3(SYNE2):c.17202C>A(p.Leu5734=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 1,612,700 control chromosomes in the GnomAD database, including 85,557 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.34 (8715 hom., cov: 32)
  • Exomes 𝑓: 0.32 (76842 hom.)
• Consequence: SYNE2 NM_182914.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 0.220

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]

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]

ACMG classification

Verdict is Benign. Variant got -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BP6: Variant 14-64170429-C-A is Benign according to our data. Variant chr14-64170429-C-A is described in ClinVar as [Benign]. Clinvar id is 130485.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr14-64170429-C-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=0.22 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYNE2	NM_182914.3	c.17202C>A	p.Leu5734=	synonymous_variant	94/116	ENST00000555002.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYNE2	ENST00000555002.6	c.17202C>A	p.Leu5734=	synonymous_variant	94/116	1	NM_182914.3	P4

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50949 AN: 151914 Hom.: 8715 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.318

GnomAD3 exomes AF: 0.329 AC: 81919 AN: 249010 Hom.: 14088 AF XY: 0.327 AC XY: 44041 AN XY: 134624

Gnomad AFR exome AF: 0.358

Gnomad AMR exome AF: 0.260

Gnomad ASJ exome AF: 0.376

Gnomad EAS exome AF: 0.572

Gnomad SAS exome AF: 0.286

Gnomad FIN exome AF: 0.328

Gnomad NFE exome AF: 0.315

Gnomad OTH exome AF: 0.314

GnomAD4 exome AF: 0.321 AC: 469584 AN: 1460668 Hom.: 76842 Cov.: 47 AF XY: 0.321 AC XY: 233105 AN XY: 726548

Gnomad4 AFR exome AF: 0.353

Gnomad4 AMR exome AF: 0.266

Gnomad4 ASJ exome AF: 0.367

Gnomad4 EAS exome AF: 0.540

Gnomad4 SAS exome AF: 0.287

Gnomad4 FIN exome AF: 0.332

Gnomad4 NFE exome AF: 0.316

Gnomad4 OTH exome AF: 0.330

GnomAD4 genome AF: 0.335 AC: 50975 AN: 152032 Hom.: 8715 Cov.: 32 AF XY: 0.336 AC XY: 24952 AN XY: 74312

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.314

Alfa AF: 0.326 Hom.: 20992

Bravo AF: 0.336

Asia WGS AF: 0.371 AC: 1287 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Emery-Dreifuss muscular dystrophy 5, autosomal dominant Benign:3

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 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	Genome-Nilou Lab	Jul 15, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Aug 15, 2013

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	6.3
Dann	Benign	0.76

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

Other links and lift over

dbSNP: rs7161192; hg19: chr14-64637147;