NM_003098.3:c.784A>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2

The NM_003098.3(SNTA1):c.784A>C(p.Thr262Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,613,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00039 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00023 ( 0 hom. )

Consequence

SNTA1
NM_003098.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3B:3

Conservation

PhyloP100: 2.17

Publications

7 publications found

Variant links:

Genes affected

SNTA1 (HGNC:11167): (syntrophin alpha 1) Syntrophins are cytoplasmic peripheral membrane scaffold proteins that are components of the dystrophin-associated protein complex. This gene is a member of the syntrophin gene family and encodes the most common syntrophin isoform found in cardiac tissues. The N-terminal PDZ domain of this syntrophin protein interacts with the C-terminus of the pore-forming alpha subunit (SCN5A) of the cardiac sodium channel Nav1.5. This protein also associates cardiac sodium channels with the nitric oxide synthase-PMCA4b (plasma membrane Ca-ATPase subtype 4b) complex in cardiomyocytes. This gene is a susceptibility locus for Long-QT syndrome (LQT) - an inherited disorder associated with sudden cardiac death from arrhythmia - and sudden infant death syndrome (SIDS). This protein also associates with dystrophin and dystrophin-related proteins at the neuromuscular junction and alters intracellular calcium ion levels in muscle tissue. [provided by RefSeq, Jan 2013]

SNTA1 Gene-Disease associations (from GenCC):

long QT syndrome 12
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
long QT syndrome
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

SNTA1 links:

LOC124904889 (HGNC:):

LOC124904889 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0937193).

BP6

Variant 20-33412700-T-G is Benign according to our data. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528. Variant chr20-33412700-T-G is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 180528.

BS2

High AC in GnomAd4 at 59 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SNTA1	NM_003098.3 link	c.784A>C	p.Thr262Pro	missense_variant	Exon 4 of 8	ENST00000217381.3	NP_003089.1	Q13424-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SNTA1	ENST00000217381.3 link	c.784A>C	p.Thr262Pro	missense_variant	Exon 4 of 8	1	NM_003098.3	ENSP00000217381.2		Q13424-1
ENSG00000288878	ENST00000785672.1 link	n.224+2466T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.000388

AC:

AN:

152120

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000483

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000647

Gnomad OTH

AF:

0.000955

GnomAD2 exomes

AF:

0.000263

AC:

AN:

250854

AF XY:

0.000273

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000398

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000509

Gnomad NFE exome

AF:

0.000406

Gnomad OTH exome

AF:

0.000326

GnomAD4 exome

AF:

0.000233

AC:

340

AN:

1461454

Hom.:

Cov.:

AF XY:

0.000243

AC XY:

177

AN XY:

727062

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.000497

AC:

AN:

26134

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86240

European-Finnish (FIN)

AF:

0.000829

AC:

AN:

53088

Middle Eastern (MID)

AF:

0.000173

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.000246

AC:

273

AN:

1111944

Other (OTH)

AF:

0.000149

AC:

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

120

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000388

AC:

AN:

152238

Hom.:

Cov.:

AF XY:

0.000443

AC XY:

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0000481

AC:

AN:

41542

American (AMR)

AF:

0.00

AC:

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5170

South Asian (SAS)

AF:

0.00

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.00104

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000647

AC:

AN:

68018

Other (OTH)

AF:

0.000945

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000457

Hom.:

Bravo

AF:

0.000204

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000233

AC:

ExAC

AF:

0.000313

AC:

EpiCase

AF:

0.000436

EpiControl

AF:

0.000415

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:3Benign:3

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Uncertain:1Benign:1

Jun 24, 2013

Biesecker Lab/Clinical Genomics Section, National Institutes of Health

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:research

- -

Apr 30, 2019

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 20009079, 21454796, 23465283) -

Long QT syndrome 12

Uncertain:1

Mar 30, 2021

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

SNTA1 NM_003098.2 exon 4 p.Thr262Pro (c.784A>C): This variant has been reported in the literature in one SIDS case (Cheng 2009 PMID:20009079). However, this variant is also present in 0.05% (14/25086) of Finnish alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/20-32000506-T-G) and is present in ClinVar (Variation ID:180528). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. Functional studies have shown that this variant causes a significant depolarizing shift in inactivation, but overall was determined to not significantly perturb cardiac sodium channel function (Cheng 2009 PMID:20009079). In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. -

Long QT syndrome

Uncertain:1

Oct 28, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 262 of the SNTA1 protein (p.Thr262Pro). This variant is present in population databases (rs200316080, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with sudden infant death syndrome (PMID: 20009079). ClinVar contains an entry for this variant (Variation ID: 180528). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SNTA1 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects SNTA1 function (PMID: 20009079). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

not specified

Benign:1

Nov 27, 2015

Blueprint Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Cardiovascular phenotype

Benign:1

May 21, 2022

Ambry Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.32

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.62

DEOGEN2

Uncertain

0.42

Eigen

Benign

-0.71

Eigen_PC

Benign

-0.60

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.21

M_CAP

Benign

0.034

MetaRNN

Benign

0.094

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.69

PhyloP100

2.2

PrimateAI

Benign

0.26

PROVEAN

Benign

-1.6

REVEL

Benign

0.044

Sift

Benign

0.26

Sift4G

Benign

0.25

Polyphen

0.016

Vest4

0.26

MVP

0.46

MPC

0.37

ClinPred

0.012

GERP RS

2.0

Varity_R

0.25

gMVP

0.71

Mutation Taster

=79/21

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over