Variant rs17082448 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_182961.4(SYNE1):c.16572+32G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0505 in 1,613,796 control chromosomes in the GnomAD database, including 3,145 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 887 hom., cov: 32)

Exomes 𝑓: 0.047 ( 2258 hom. )

Consequence

SYNE1
NM_182961.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.274

Variant links:

Genes affected

SYNE1 (HGNC:17089): (spectrin repeat containing nuclear envelope protein 1) This gene encodes a spectrin repeat containing protein expressed in skeletal and smooth muscle, and peripheral blood lymphocytes, that localizes to the nuclear membrane. Mutations in this gene have been associated with autosomal recessive spinocerebellar ataxia 8, also referred to as autosomal recessive cerebellar ataxia type 1 or recessive ataxia of Beauce. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

SYNE1 links:

SYNE1 (HGNC:):

SYNE1 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=-0.91).

BP6

Variant 6-152318049-C-G is Benign according to our data. Variant chr6-152318049-C-G is described in ClinVar as [Benign]. Clinvar id is 262169.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SYNE1	NM_182961.4 linkuse as main transcript	c.16572+32G>C		intron_variant		ENST00000367255.10	NP_892006.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SYNE1	ENST00000367255.10 linkuse as main transcript	c.16572+32G>C		intron_variant		1	NM_182961.4	ENSP00000356224.5		Q8NF91-1

Frequencies

GnomAD3 genomes

AF:

0.0818

AC:

12434

AN:

152094

Hom.:

881

Cov.:

show subpopulations

Gnomad AFR

AF:

0.197

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.0335

Gnomad ASJ

AF:

0.0389

Gnomad EAS

AF:

0.0266

Gnomad SAS

AF:

0.0516

Gnomad FIN

AF:

0.0148

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.0426

Gnomad OTH

AF:

0.0640

GnomAD3 exomes

AF:

0.0462

AC:

11566

AN:

250350

Hom.:

496

AF XY:

0.0446

AC XY:

6036

AN XY:

135460

show subpopulations

Gnomad AFR exome

AF:

0.199

Gnomad AMR exome

AF:

0.0214

Gnomad ASJ exome

AF:

0.0420

Gnomad EAS exome

AF:

0.0284

Gnomad SAS exome

AF:

0.0479

Gnomad FIN exome

AF:

0.0154

Gnomad NFE exome

AF:

0.0410

Gnomad OTH exome

AF:

0.0374

GnomAD4 exome

AF:

0.0473

AC:

69061

AN:

1461584

Hom.:

2258

Cov.:

AF XY:

0.0463

AC XY:

33666

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.210

Gnomad4 AMR exome

AF:

0.0239

Gnomad4 ASJ exome

AF:

0.0409

Gnomad4 EAS exome

AF:

0.0323

Gnomad4 SAS exome

AF:

0.0454

Gnomad4 FIN exome

AF:

0.0157

Gnomad4 NFE exome

AF:

0.0453

Gnomad4 OTH exome

AF:

0.0532

GnomAD4 genome

AF:

0.0819

AC:

12467

AN:

152212

Hom.:

887

Cov.:

AF XY:

0.0795

AC XY:

5915

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.197

Gnomad4 AMR

AF:

0.0334

Gnomad4 ASJ

AF:

0.0389

Gnomad4 EAS

AF:

0.0265

Gnomad4 SAS

AF:

0.0514

Gnomad4 FIN

AF:

0.0148

Gnomad4 NFE

AF:

0.0425

Gnomad4 OTH

AF:

0.0638

Alfa

AF:

0.0585

Hom.:

Bravo

AF:

0.0877

Asia WGS

AF:

0.0550

AC:

190

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.90

DANN

Benign

0.47

Splicing

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