rs214968

chr6-152455615-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_182961.4(SYNE1):c.2728-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,611,340 control chromosomes in the GnomAD database, including 48,352 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.27 (5955 hom., cov: 33)
  • Exomes 𝑓: 0.24 (42397 hom.)
• Consequence: SYNE1 NM_182961.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0830

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 6-152455615-G-A is Benign according to our data. Variant chr6-152455615-G-A is described in ClinVar as [Benign]. Clinvar id is 262195.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-152455615-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SYNE1	NM_182961.4	c.2728-25C>T		intron_variant		ENST00000367255.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SYNE1	ENST00000367255.10	c.2728-25C>T		intron_variant		1	NM_182961.4	P1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41189 AN: 151982 Hom.: 5948 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.274

GnomAD3 exomes AF: 0.251 AC: 63081 AN: 251076 Hom.: 8333 AF XY: 0.252 AC XY: 34141 AN XY: 135736

Gnomad AFR exome AF: 0.371

Gnomad AMR exome AF: 0.213

Gnomad ASJ exome AF: 0.222

Gnomad EAS exome AF: 0.335

Gnomad SAS exome AF: 0.287

Gnomad FIN exome AF: 0.187

Gnomad NFE exome AF: 0.238

Gnomad OTH exome AF: 0.245

GnomAD4 exome AF: 0.236 AC: 344897 AN: 1459242 Hom.: 42397 Cov.: 31 AF XY: 0.238 AC XY: 172975 AN XY: 726124

Gnomad4 AFR exome AF: 0.366

Gnomad4 AMR exome AF: 0.218

Gnomad4 ASJ exome AF: 0.229

Gnomad4 EAS exome AF: 0.351

Gnomad4 SAS exome AF: 0.286

Gnomad4 FIN exome AF: 0.185

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.248

GnomAD4 genome AF: 0.271 AC: 41232 AN: 152098 Hom.: 5955 Cov.: 33 AF XY: 0.268 AC XY: 19887 AN XY: 74342

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.275

Alfa AF: 0.261 Hom.: 1106

Bravo AF: 0.281

Asia WGS AF: 0.292 AC: 1018 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

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- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.31
Dann	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs214968; hg19: chr6-152776750; COSMIC: COSV54990723; COSMIC: COSV54990723;