chr3-38613799-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BS1BS2
The NM_000335.5(SCN5A):c.647C>T(p.Ser216Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,610,920 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00067 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 3 hom. )
Consequence
SCN5A
NM_000335.5 missense
NM_000335.5 missense
Scores
13
3
3
Clinical Significance
Conservation
PhyloP100: 10.0
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 Benign. Variant got -7 ACMG points.
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.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00067 (102/152338) while in subpopulation AMR AF= 0.00157 (24/15310). AF 95% confidence interval is 0.00108. There are 0 homozygotes in gnomad4. There are 49 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 3 SD gene
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SCN5A | ENST00000423572.7 | c.647C>T | p.Ser216Leu | missense_variant | Exon 6 of 28 | 1 | NM_000335.5 | ENSP00000398266.2 | ||
| SCN5A | ENST00000413689.6 | c.703+176C>T | intron_variant | Intron 6 of 27 | 5 | NM_001099404.2 | ENSP00000410257.1 |
Frequencies
GnomAD3 genomes 0.000670 AC: 102AN: 152220Hom.: 0 Cov.: 33
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GnomAD4 genome 0.000670 AC: 102AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.000658 AC XY: 49AN XY: 74496
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:13Benign:14Other:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:2Benign:7Other:1
| Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
| Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 02, 2025 | - - |
| Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
| Uncertain significance, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The SCN5A p.Ser216Leu variant was identified in 12 of 6956 proband chromosomes (freq: 0.00173) from individuals or families with familial cardiovascular disease, sudden cardiac death, Brugada syndrome and Long QT syndrome and 8 of 5200 control chromosomes (freq: 0.002) (Seidelmann_2017_PMID: 28087566, Methner_2016_PMID: 27435932, Ortiz-Bonnin_2016_PMID: 27287068, Adler_2016_PMID: 26743238, Riuro_2015_PMID: 24667783, Olesen_2012_PMID: 22685113, Crotti_2012_PMID: 22840528, Kapplinger_2010_PMID: 20129283). The variant was also identified in dbSNP (ID: rs41276525), ClinVar (conflicting interpretations of pathogenicity; classified likely benign by Invitae and Integrated genetics, and VUS by Laboratory for Molecular Medicine, GeneDx and Ambry Genetics; associated conditions are Brugada syndrome, arrhythmia, and cardiovascular phenotype), and LOVD 3.0. The variant was not identified in Cosmic. The variant was found in control databases in 181 of 275296 chromosomes (1 homozygous in the South Asian population) at a frequency of 0.000657 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 126 of 126006 chromosomes (freq: 0.001), Ashkenazi Jewish in 10 of 10216 chromosomes (freq: 0.000979), Latino in 22 of 34780 chromosomes (freq: 0.000633), South Asian in 17 of 29594 chromosomes (freq: 0.000574), Other in 4 of 7056 chromosomes (freq: 0.000567), African in 1 of 23612 chromosomes (freq: 0.000042) and European (Finnish) in 1 of 24754 chromosomes (freq: 0.00004), while the variant was not observed in the East Asian population. In vitro electrophysiological studies performed using the two-electrode voltage-clamp technique (TEVC) in Xenopus laevis oocytes showed that the S216L variant has the potential to cause 60% reduction in maximum Na(+) current (I(Na)) density and a QT interval prolongation (Ortiz-Bonnin_2016_PMID: 27287068; Marangoni_2011_PMID: 21705349). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Ser216 residue is conserved in mammals but not in more distantly related organisms, and four out of five computational analyses (PolyPhen-2, SIFT, BLOSUM, MutationTaster) suggest that the S variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. - |
| Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
| not provided, no classification provided | literature only | Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust | - | This variant has been reported in the following publications (PMID:15851227;PMID:17210839;PMID:19412328;PMID:19841300;PMID:20129283;PMID:21705349). - |
| Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 25, 2019 | The SCN5A c.647C>T; p.Ser216Leu variant (rs41276525) is reported in the literature in individuals and families affected with dilated cardiomyopathy, Brugada syndrome, long QT syndrome, or arrhythmias (Hershberger 2008, Marangoni 2011, Olesen 2012, Ortiz-Bonnin 2016). However, this variant has also been observed in healthy control individuals (Kapplinger 2010), and one study observed no significant difference in QT interval of individuals with and without the variant (Ghouse 2015). This variant is found in the non-Finnish European population with an overall allele frequency of 0.10% (126/126006 alleles) in the Genome Aggregation Database. The serine at codon 216 is highly conserved, computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious, and functional analyses indicate an increased current density relative to wildtype protein (Marangoni 2011, Ortiz-Bonnin 2016). However, due to conflicting information, the clinical significance of the p.Ser216Leu variant is uncertain at this time. References: Ghouse J et al. Rare genetic variants previously associated with congenital forms of long QT syndrome have little or no effect on the QT interval. Eur Heart J. 2015 Oct 1;36(37):2523-9. Hershberger RE et al. Coding sequence mutations identified in MYH7, TNNT2, SCN5A, CSRP3, LBD3, and TCAP from 313 patients with familial or idiopathic dilated cardiomyopathy. Clin Transl Sci. 2008 May;1(1):21-6. Kapplinger JD et al. An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing. Heart Rhythm. 2010 Jan;7(1):33-46. Marangoni S et al. A Brugada syndrome mutation (p.S216L) and its modulation by p.H558R polymorphism: standard and dynamic characterization. Cardiovasc Res. 2011 Sep 1;91(4):606-16. Olesen MS et al. High prevalence of long QT syndrome-associated SCN5A variants in patients with early-onset lone atrial fibrillation. Circ Cardiovasc Genet. 2012 Aug 1;5(4):450-9. Ortiz-Bonnin B et al. Electrophysiological characterization of a large set of novel variants in the SCN5A-gene: identification of novel LQTS3 and BrS mutations. Pflugers Arch. 2016 Aug;468(8):1375-87. - |
| Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 21, 2021 | This variant is associated with the following publications: (PMID: 30356750, 30677491, 19412328, 15851227, 21705349, 17210841, 23414114, 22378279, 23158531, 22685113, 20129283, 23465283, 23299917, 18378609, 23272275, 22677073, 17210839, 24136861, 23321620, 24667783, 26406308, 22337857, 26159999, 25904541, 27287068, 25554238, 28316956, 26916278, 28341588, 29672598, 31043699, 30847666, 33131149, 32880476) - |
not specified Uncertain:1Benign:2
| Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 07, 2014 | The p.Ser216Leu variant in SCN5A has been reported in 2 individuals with DCM, 2 individuals with atrial fibrillation, 1 individual with Brugada syndrome, and 1 infant with sudden infant death syndrome (Arnestad 2007, Hershberger 2008, Maran goni 2011, Olesen 2012). In addition, this variant has been identified in 0.3% ( 6/1888) of healthy Caucasian chromosomes (Ackerman 2004, Kapplinger 2010) and in 0.1% (11/8432) of European American chromosomes by the NHLBI Exome Sequencing P roject (http://evs.gs.washington.edu/EVS/; dbSNP rs41276525). Additionally, comp utational prediction tools and conservation analysis suggest that this variant m ay impact the protein, though this information is not predictive enough to deter mine pathogenicity. Finally, in vitro functional studies provide some evidence t hat the p.Ser216Leu variant may impact protein function (Wang 2007, Marangoni 20 11). However, these types of assays may not accurately represent biological func tion. In summary, there is conflicting evidence on the p.Ser216Leu variant and i ts clinical significance is uncertain. - |
| Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Apr 08, 2019 | Variant summary: SCN5A c.647C>T (p.Ser216Leu) results in a non-conservative amino acid change located in the Voltage-dependent channel domain superfamily (IPR027359) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00068 in 280270 control chromosomes, predominantly at a frequency of 0.00099 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 10 fold of the estimated maximal expected allele frequency for a pathogenic variant in SCN5A causing Arrhythmia phenotype (0.0001), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.647C>T has been reported in the literature in multiple testing cohorts among individuals with borderline or with elevated QT intervals. Several of these studies predate as well as postdate the emergence of large scale control datasets such as ExAC and gnomad. Furthermore, several of these studies reported a classification of this variant as a VUS (example Seidelmann_2017, Riuro_2015, Ortiz-Bonnin_2016). Therefore, no firm conclusions can be drawn from these data. In addition, the variant was identified in multiple healthy individuals with no history of arrhythmias or other cardiac diseases and normal ECG (Refsgaard_2012; Crotti_2012; Kapplinger_2010) and was shown to not segregate with disease (Marangoni_2011; Riuro_2015). Co-occurrences with other pathogenic variant(s) have been reported in the literature (KCNQ1) as well as our internal testing (SCN5A) experience (KCNQ1 c.686G>A, p.Gly229Asp; SCN5A c.535C>T, p.R179*), providing supporting evidence for a benign role. Several publications report experimental evidence evaluating an impact on protein function, at-least one of which concluded that the variant should remain as a variant of unknown significance due to inconclusive findings (example Ortiz-Bonnin_SCN5A_EJP_2016). Other publications reporting a functional impact present findings that are not firmly correlated to in-vivo mechanisms of disease (ex Wang_2007 and Marangoni_2011). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and one of these reported a classification of likely benign. Based on the evidence outlined above, the variant was classified as benign. - |
Sick sinus syndrome 1 Uncertain:2
| Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Oct 10, 2019 | This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PP3,BS2. - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 01, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Long QT syndrome 3 Uncertain:2
| Uncertain significance, criteria provided, single submitter | clinical testing | KardioGenetik, Herz- und Diabeteszentrum NRW | Jun 26, 2024 | PP3, BS1 - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 01, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Dilated cardiomyopathy 1E Uncertain:1Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Feb 02, 2022 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as likely benign. Following criteria are met: 0103 - Loss of function and gain of function are both known mechanisms of disease in this gene. Loss of function is usually associated with Brugada syndrome 1 (MIM#601144) and sick sinus syndrome 1 (SSS) (MIM#608567), whereas gain of function is usually associated with long QT syndrome-3 (LQTS) (MIM#603830). Dilated cardiomyopathy 1E (DCM) (MIM#601154) can be caused by variants with either a loss or gain of function mechanism (PMID: 29798782). However, some variants simultaneously result in both a loss and gain of function effect, and have been observed in patients with LQTS, Brugada or SSS, and patients with a blended phenotype. Additionally, different studies have shown conflicting mechanisms in association with familial atrial fibrillation 10 (MIM#614022) (PMIDs: 29806494, 19167345, 26798387, 29798782). (I) 0108 - This gene is associated with both recessive and dominant disease. Most conditions associated with this gene are dominantly inherited, however SSS is caused by biallelic variants (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from serine to leucine. (I) 0251 - This variant is heterozygous. (I) 0308 - Population frequency for this variant is out of keeping with known incidence of SCN5A-related disorders, gnomAD v2: 179 heterozygotes, 1 homozygote. (SB) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated S3 to S4 extracellular linker in ion transport domain I (Uniprot). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been previously reported in individuals with idiopathic dilated cardiomyopathy, LQTS, Brugada syndrome, sudden infant death syndrome (SIDS), and sudden unexplained death. However, the variant is generally classified as either likely benign or a VUS (PMIDs: 19412328, 27287068, 21705349, 17210839, 31043699, 22677073, ClinVar, VCGS). Additionally, this variant has been identified in healthy control individuals (PMID: 20129283). (I) 1010 - Functional evidence for this variant is conflicting. Patch clamp functional assays have reported that this variant causes a gain-of-function, however, the gain-of-function mechanism varies between functional studies (PMIDs: 17210841, 21705349, 27287068). Patch clamp assays have been shown to be unreliable, therefore results from these studies are used with caution during variant classification. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 01, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Cardiac arrhythmia Benign:2
| Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jun 18, 2019 | - - |
| Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Sep 27, 2024 | - - |
Brugada syndrome 1 Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 01, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Ventricular fibrillation, paroxysmal familial, type 1 Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 01, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
SUDDEN INFANT DEATH SYNDROME;C1832680:Dilated cardiomyopathy 1E;C1837845:Sick sinus syndrome 1;C1859062:Long QT syndrome 3;C1879286:Progressive familial heart block, type 1A;C2751898:Ventricular fibrillation, paroxysmal familial, type 1;C3151464:Atrial fibrillation, familial, 10;C4551804:Brugada syndrome 1 Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Mar 30, 2021 | SCN5A NM_198056.2 exon 6 p.Ser216Leu (c.647C>T): This variant has been reported in the literature in several individuals with various cardiac phenotypes (DCM, BrS, LQTS, Afib) (Hershberger 2008 PMID:19412328, Marangoni 2011 PMID:21705349, Crotti 2012 PMID:23158531, Olesen 2012 PMID:22685113, Riuro 2015 PMID:24667783). This variant has also been reported in a SIDS case and in a SUD case of an individual with a history of epilepsy (Wang 2007 PMID:17210841, Marcondes 2018 PMID:29672598). However, this variant is also present in 0.1% (126/126006) of European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/3-38655290-G-A) and is present in ClinVar (Variation ID:36767). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In addition, functional studies have shown a deleterious effect of this variant (Wang 2007 PMID:17210841, Marangoni 2011 PMID:21705349). However, these studies may not accurately represent in vivo biological function. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Brugada syndrome Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals | Jan 18, 2021 | - - |
Progressive familial heart block, type 1A Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | May 01, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Ventricular tachycardia Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego | Mar 04, 2019 | - - |
Cardiovascular phenotype Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 07, 2021 | 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
CardioboostCm
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Pathogenic
.;D;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;M;.
PROVEAN
Pathogenic
D;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D
Sift4G
Benign
T;T;T
Polyphen
D;P;.
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at