rs12720452

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 5P and 2B. PM2PM5PP2BP4_Moderate

The NM_000335.5(SCN5A):​c.1844G>C​(p.Gly615Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G615E) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 32)

Consequence

SCN5A
NM_000335.5 missense

Scores

5
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.210
Variant links:
Genes affected
SCN5A (HGNC:10593): (sodium voltage-gated channel alpha subunit 5) The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene have been associated with long QT syndrome type 3 (LQT3), atrial fibrillation, cardiomyopathy, and Brugada syndrome 1, all autosomal dominant cardiac diseases. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr3-38603758-C-T is described in Lovd as [Pathogenic].
PP2
Missense variant in the SCN5A gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 99 curated pathogenic missense variants (we use a threshold of 10). The gene has 60 curated benign missense variants. Gene score misZ: 2.7504 (below the threshold of 3.09). Trascript score misZ: 4.8279 (above the threshold of 3.09). GenCC associations: The gene is linked to progressive familial heart block, type 1A, Brugada syndrome, familial sick sinus syndrome, short QT syndrome, paroxysmal familial ventricular fibrillation, progressive familial heart block, long QT syndrome 3, familial atrial fibrillation, catecholaminergic polymorphic ventricular tachycardia, dilated cardiomyopathy, dilated cardiomyopathy 1E, arrhythmogenic right ventricular cardiomyopathy, Brugada syndrome 1, atrial standstill, familial isolated dilated cardiomyopathy, familial long QT syndrome, sick sinus syndrome 1.
BP4
Computational evidence support a benign effect (MetaRNN=0.10316634).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCN5ANM_001099404.2 linkc.1844G>C p.Gly615Ala missense_variant Exon 12 of 28 ENST00000413689.6 NP_001092874.1 Q14524H9KVD2
SCN5ANM_000335.5 linkc.1844G>C p.Gly615Ala missense_variant Exon 12 of 28 ENST00000423572.7 NP_000326.2 Q14524-2Q86V90

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCN5AENST00000413689.6 linkc.1844G>C p.Gly615Ala missense_variant Exon 12 of 28 5 NM_001099404.2 ENSP00000410257.1 H9KVD2
SCN5AENST00000423572.7 linkc.1844G>C p.Gly615Ala missense_variant Exon 12 of 28 1 NM_000335.5 ENSP00000398266.2 Q14524-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.085
CardioboostCm
Benign
0.0025
BayesDel_addAF
Uncertain
0.060
T
BayesDel_noAF
Benign
-0.15
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.46
.;.;.;.;.;T;.;.;.
Eigen
Benign
-0.45
Eigen_PC
Benign
-0.35
FATHMM_MKL
Benign
0.28
N
LIST_S2
Benign
0.75
.;T;T;T;T;T;T;.;T
M_CAP
Uncertain
0.17
D
MetaRNN
Benign
0.10
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.35
T
MutationAssessor
Benign
1.1
.;L;.;.;.;L;.;.;.
PrimateAI
Benign
0.39
T
PROVEAN
Benign
-0.92
N;N;N;N;N;N;N;N;N
REVEL
Uncertain
0.41
Sift
Benign
0.34
T;T;T;T;T;T;T;T;T
Sift4G
Benign
0.70
T;T;T;T;T;T;T;T;T
Polyphen
0.0050
B;B;.;B;.;B;B;.;.
Vest4
0.15
MutPred
0.24
Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);Gain of glycosylation at P614 (P = 0.1711);
MVP
0.81
MPC
0.56
ClinPred
0.21
T
GERP RS
4.2
Varity_R
0.10
gMVP
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-38645249; API