Variant 14-64087370-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_182914.3(SYNE2):c.11485-301G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0348 in 551,250 control chromosomes in the GnomAD database, including 464 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 108 hom., cov: 32)

Exomes 𝑓: 0.036 ( 356 hom. )

Consequence

SYNE2
NM_182914.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.272

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 (BayesDel_noAF=-0.9).

BP6

Variant 14-64087370-G-A is Benign according to our data. Variant chr14-64087370-G-A is described in ClinVar as [Benign]. Clinvar id is 1291221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNE2	NM_182914.3 linkuse as main transcript	c.11485-301G>A		intron_variant		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.11485-301G>A		intron_variant		1	NM_182914.3	ENSP00000450831	P4	Q8WXH0-2

Frequencies

GnomAD3 genomes

AF:

0.0313

AC:

4762

AN:

151906

Hom.:

108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00837

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0655

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.0501

Gnomad SAS

AF:

0.0277

Gnomad FIN

AF:

0.0608

Gnomad MID

AF:

0.00323

Gnomad NFE

AF:

0.0333

Gnomad OTH

AF:

0.0282

GnomAD3 exomes

AF:

0.0378

AC:

8683

AN:

229610

Hom.:

228

AF XY:

0.0363

AC XY:

4548

AN XY:

125424

show subpopulations

Gnomad AFR exome

AF:

0.00837

Gnomad AMR exome

AF:

0.0798

Gnomad ASJ exome

AF:

0.0144

Gnomad EAS exome

AF:

0.0485

Gnomad SAS exome

AF:

0.0319

Gnomad FIN exome

AF:

0.0498

Gnomad NFE exome

AF:

0.0304

Gnomad OTH exome

AF:

0.0345

GnomAD4 exome

AF:

0.0361

AC:

14408

AN:

399226

Hom.:

356

Cov.:

AF XY:

0.0355

AC XY:

8040

AN XY:

226326

show subpopulations

Gnomad4 AFR exome

AF:

0.00858

Gnomad4 AMR exome

AF:

0.0782

Gnomad4 ASJ exome

AF:

0.0125

Gnomad4 EAS exome

AF:

0.0500

Gnomad4 SAS exome

AF:

0.0314

Gnomad4 FIN exome

AF:

0.0498

Gnomad4 NFE exome

AF:

0.0317

Gnomad4 OTH exome

AF:

0.0317

GnomAD4 genome

AF:

0.0313

AC:

4762

AN:

152024

Hom.:

108

Cov.:

AF XY:

0.0333

AC XY:

2475

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.00834

Gnomad4 AMR

AF:

0.0655

Gnomad4 ASJ

AF:

0.0164

Gnomad4 EAS

AF:

0.0500

Gnomad4 SAS

AF:

0.0279

Gnomad4 FIN

AF:

0.0608

Gnomad4 NFE

AF:

0.0333

Gnomad4 OTH

AF:

0.0279

Alfa

AF:

0.0327

Hom.:

Bravo

AF:

0.0299

Asia WGS

AF:

0.0440

AC:

153

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 15, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.33

DANN

Benign

0.67

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