Variant rs2306056 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_001377540.1(SLMAP):c.828+11C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,447,716 control chromosomes in the GnomAD database, including 19,773 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.20 ( 3032 hom., cov: 31)

Exomes 𝑓: 0.19 ( 16741 hom. )

Consequence

SLMAP
NM_001377540.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0380

Variant links:

Genes affected

SLMAP (HGNC:16643): (sarcolemma associated protein) This gene encodes a component of a conserved striatin-interacting phosphatase and kinase complex. Striatin family complexes participate in a variety of cellular processes including signaling, cell cycle control, cell migration, Golgi assembly, and apoptosis. The protein encoded by this gene is a coiled-coil, tail-anchored membrane protein with a single C-terminal transmembrane domain that is posttranslationally inserted into membranes. Mutations in this gene are associated with Brugada syndrome, a cardiac channelopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]

SLMAP 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=-0.85).

BP6

Variant 3-57860850-C-A is Benign according to our data. Variant chr3-57860850-C-A is described in ClinVar as [Benign]. Clinvar id is 260135.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-57860850-C-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLMAP	NM_001377540.1 linkuse as main transcript	c.828+11C>A		intron_variant		ENST00000671191.1	NP_001364469.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLMAP	ENST00000671191.1 linkuse as main transcript	c.828+11C>A		intron_variant			NM_001377540.1	ENSP00000499458	P4

Frequencies

GnomAD3 genomes

AF:

0.200

AC:

29582

AN:

147764

Hom.:

3031

Cov.:

show subpopulations

Gnomad AFR

AF:

0.182

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.243

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.436

Gnomad SAS

AF:

0.132

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.191

Gnomad OTH

AF:

0.213

GnomAD3 exomes

AF:

0.261

AC:

37806

AN:

144904

Hom.:

2109

AF XY:

0.257

AC XY:

20244

AN XY:

78742

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.367

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.451

Gnomad SAS exome

AF:

0.181

Gnomad FIN exome

AF:

0.193

Gnomad NFE exome

AF:

0.246

Gnomad OTH exome

AF:

0.250

GnomAD4 exome

AF:

0.193

AC:

251013

AN:

1299842

Hom.:

16741

Cov.:

AF XY:

0.192

AC XY:

123911

AN XY:

646156

show subpopulations

Gnomad4 AFR exome

AF:

0.173

Gnomad4 AMR exome

AF:

0.280

Gnomad4 ASJ exome

AF:

0.184

Gnomad4 EAS exome

AF:

0.377

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.173

Gnomad4 NFE exome

AF:

0.190

Gnomad4 OTH exome

AF:

0.196

GnomAD4 genome

AF:

0.200

AC:

29609

AN:

147874

Hom.:

3032

Cov.:

AF XY:

0.201

AC XY:

14425

AN XY:

71906

show subpopulations

Gnomad4 AFR

AF:

0.182

Gnomad4 AMR

AF:

0.243

Gnomad4 ASJ

AF:

0.194

Gnomad4 EAS

AF:

0.436

Gnomad4 SAS

AF:

0.132

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.191

Gnomad4 OTH

AF:

0.214

Alfa

AF:

0.0399

Hom.:

Bravo

AF:

0.207

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	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 15, 2024	- -

Brugada syndrome

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Phosphorus, Inc.	Aug 01, 2017	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 16, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.2

DANN

Benign

0.31

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