rs483352835

Positions:

• chr1-201362395-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PVS1_Moderate BS2

The NM_001276345.2(TNNT2):​c.601-1G>A variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0000075 (0 hom.)
• Consequence: TNNT2 NM_001276345.2 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:17 B:1
• Conservation: PhyloP100: 2.32

Genes affected

TNNT2 (HGNC:11949): (troponin T2, cardiac type) This gene encodes the cardiac isoform of troponin T. The encoded protein is the tropomyosin-binding subunit of the troponin complex, which is located on the thin filament of striated muscles and regulates muscle contraction in response to alterations in intracellular calcium ion concentration. Mutations in this gene have been associated with familial hypertrophic cardiomyopathy as well as with dilated cardiomyopathy. [provided by RefSeq, May 2022]

TNNT2 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.008918618 fraction of the gene. Cryptic splice site detected, with MaxEntScore 7.6, offset of 3, new splice context is: atggtttcccggtttaacAGgcc. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• BS2: High AC in GnomAdExome4 at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNNT2	NM_001276345.2	c.601-1G>A		splice_acceptor_variant, intron_variant		ENST00000656932.1	NP_001263274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNNT2	ENST00000656932.1	c.601-1G>A		splice_acceptor_variant, intron_variant			NM_001276345.2	ENSP00000499593.1

Frequencies

GnomAD3 genomes AF: 0.0000131 AC: 2 AN: 152188 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.0000201 AC: 5 AN: 249022 Hom.: 0 AF XY: 0.00000742 AC XY: 1 AN XY: 134700

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000164

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000753 AC: 11 AN: 1461564 Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6 AN XY: 727020

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000581

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000828

GnomAD4 genome AF: 0.0000131 AC: 2 AN: 152306 Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0 AN XY: 74472

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.0000265 Hom.: 0

Bravo AF: 0.00000378

ExAC AF: 0.0000165 AC: 2

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:17 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Uncertain:5

Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	May 03, 2023	Identified in patients with HCM and DCM in published literature (Van Driest et al., 2004; Rani et al., 2014; Walsh et al., 2017; Mazzarotto et al., 2020); at least one patient harbored an additional pathogenic variant in a cardiomyopathy-related gene; Not observed at significant frequency in large population cohorts (gnomAD); Canonical splice site variant in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; This variant is associated with the following publications: (PMID: 24992688, 27532257, 15358028, 31983221) -
Uncertain significance, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jan 27, 2022	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Sep 30, 2010	Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. IVS 11-1G>A. This variant changes the last base of the intron for a G to an A. This base is a key part of the splicing consensus sequence and is essentially always a G. Thus a change from G to A would be highly likely to affect splicing. Consistent with this expectation, Van Driest et al (2004) reported alternative splicing causing an in-frame deletion of a glutamine in a patient with this mutation. That patient also had a mutation in MYH7 (p.Arg453Cys) and a clinical history consistent with multiple mutations (infantile onset HCM with severe hypertrophy (38mm) and VT). While most TNNT2 mutations are missense, four other single amino acid deletions have been reported in association with HCM. No segregation data on this variant were reported by either the testing lab or Van Dreist et al. The variant is not currently listed in the NHLBI Exome Sequencing Project dataset, which includes variant calls on ~5300 Caucasian and African American individuals (as of 3/6/2012). Note that this dataset does not match the patient's ancestry (Samoan). Of note, there are no splicing variants in TNNT2 in this data set. -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Dec 17, 2020	- -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -

not specified Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 11, 2015	Variant classified as Uncertain Significance - Favor Pathogenic. The c.571-1G>A variant in TNNT2 has been reported in 4 individuals with cardiomyopathy (1 child DCM; 1 child LVNC; 1 child HCM and VT; 1 adult DCM) (Van Driest 2004, Rani 2014 , LMM unpublished data). Of note, the child with HCM also carried a pathogenic v ariant in MYH7 (Van Driest 2004). It has been identified in 2/23916 Asian chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs483352835). This variant occurs in the invariant region (+/- 1,2) and h as been shown to lead to the deletion of a single amino acid (Glu) (Van Driest 2 004). A small number of similar TNNT2 variants (single amino acid deletions and splice variants) are established as pathogenic for cardiomyopathy (DCM, HCM). In summary, while there is some suspicion for a pathogenic role, the clinical sign ificance of the c.571-1G>A variant is uncertain. -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 18, 2024	Variant summary: TNNT2 c.571-1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Computational tools predict a significant impact on normal splicing: Two predict the variant abolishes a canonical 3' acceptor site. Two predict the variant creates a cryptic 3' acceptor site, and one predicts the variant strengthens a 3' acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing, however it reports that the variant results in an in-frame deletion of one amino acid (Van Driest_2004), which is consistent with the computation predictions. The variant allele was found at a frequency of 2e-05 in 249022 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.571-1G>A has been reported in the literature in individuals affected with Hypertrophic Cardiomyopathy or Dilated Cardiomyopathy without strong evidence of causality (e.g. Van Driest_2004, Rani_2014, Walsh_2017, McGurk_2023, Earle_2024). These reports do not provide unequivocal conclusions about association of the variant with Hypertrophic Cardiomyopathy. Co-occurrence with another pathogenic variant has been reported in one of these cases (MYH7 c.1357C>T, p.Arg453Cys), providing supporting evidence for a benign role. The following publications have been ascertained in the context of this evaluation (PMID: 15358028, 24992688, 27532257, 37652022, 38456273). ClinVar contains an entry for this variant (Variation ID: 132940). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Dilated cardiomyopathy 1D Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Oct 08, 2024	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0105 - The mechanism of disease for this gene is not clearly established. Functional studies have suggested loss-of-function, gain-of-function and dominant-negative mechanisms based on calcium sensitivity, contractibility and mouse models (PMID: 18612386, 32098556, 33025817). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. p.(Arg92Gln) has been reported to cause both dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM), even within the same family (PMID: 26507537). (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0219 - This variant is intronic in an alternative transcript. However, it is a canonical splice site in both the transcript predominantly reported in ClinVar and on the transcript with the highest expression in heart (GTEx). (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (5 heterozygotes, 0 homozygotes). (SP) 0311 - An alternative nucleotide change at the same canonical splice site, is present in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0508 - In silico predictions for abnormal splicing are conflicting. (I) 0705 - No comparable canonical splice site variants have previous evidence for pathogenicity. (I) 0808 - Previous reports of pathogenicity for this variant are conflicting. This variant has been reported multiple times as a VUS (ClinVar, LOVD, PMID: 27532257, PMID: 30847666) and as likely pathogenic (ClinVar; PMID:37821546). It has been reported in an individual with severe early onset hypertrophic cardiomyopathy (HCM), who also harboured the well-known pathogenic p.(Arg453Cys) variant in the MYH7 gene (PMID: 15358028). Although this variant is reported to result in an in-frame deletion of p.(Gln201del), data was not shown and methods were not specified (PMID: 15358028). Additionally, this variant was identified in individuals with DCM (VCGS, PMID: 24992688) and HCM (PMID: 15358028), and in a fetus with noncompaction cardiomyopathy (PMID: 33553264). (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1205 - This variant has been shown to be maternally inherited (by duo analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Apr 11, 2023	- -

Cardiomyopathy Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 06, 2022	This variant (also known as IVS11-1G>A) causes a G to A nucleotide substitution at the -1 position of intron 11 of the TNNT2 gene. Splice prediction tools suggest that this variant may impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has been reported in three individuals affected with dilated cardiomyopathy (PMID: 24992688, 31983221) and in several individuals affected with hypertrophic cardiomyopathy (PMID: 15358028, 27532257, 30847666). One of the individuals affected with hypertrophic cardiomyopathy carried a pathogenic p.Arg453His in the MYH7 gene that could explain the observed phenotype. This variant has been identified in 5/249022 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	Jun 17, 2024	This variant (also known as IVS11-1G>A) causes a G to A nucleotide substitution at the -1 position of intron 11 of the TNNT2 gene. Splice prediction tools suggest that this variant may impact RNA splicing. A functional study using patient-derived tissue for RNA analysis reported that this variant causes an in-frame deletion of one amino acid, however data was not shown (PMID: 15358028), and clinical relevance of this observation is unclear. This variant has been reported in eight individuals affected with hypertrophic cardiomyopathy (PMID: 15358028, 27532257, 30847666, 33495597, 37821546); one of these individuals also carried a pathogenic variant in the MYH7 gene (PMID: 15358028). This variant has also been reported in three individuals affected with dilated cardiomyopathy (PMID: 24992688, 31983221), in one individual affected with noncompaction cardiomyopathy (PMID: 33553264), and in three individuals affected with sudden unexplained death (PMID: 37821546). This variant has been identified in 5/249022 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Dilated cardiomyopathy 1D;C1861864:Hypertrophic cardiomyopathy 2;C2676271:Cardiomyopathy, familial restrictive, 3 Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 09, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 09, 2024	This sequence change affects an acceptor splice site in intron 11 of the TNNT2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), however the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in TNNT2 cause disease. This variant is present in population databases (rs483352835, gnomAD 0.01%). Disruption of this splice site has been observed in individual(s) with clinical features of TNNT2-related conditions (PMID: 24992688, 27532257). ClinVar contains an entry for this variant (Variation ID: 132940). 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. -

Dilated cardiomyopathy 1DD Uncertain:1

Uncertain significance, no assertion criteria provided

not provided

Evolutionary and Medical Genetics Laboratory, Centre for Cellular and Molecular Biology

-

- -

Cardiomyopathy, familial restrictive, 3 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Hypertrophic cardiomyopathy 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 12, 2021

The c.571-1G>A intronic alteration consists of a G to A substitution 1 nucleotides before coding exon 11 in the TNNT2 gene. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Hypertrophic cardiomyopathy Benign:1

Benign, criteria provided, single submitter

curation;literature only

Ingles Laboratory, Garvan Institute Of Medical Research

Mar 26, 2024

We identified TNNT2; NM_001001430.3: c.571-1G>A (rs483352835) in 2 probands. Proband 1 was a male of Oceanian ancestry SCD in his early 20s with no cause identified following a comprehensive post-mortem investigation. Proband 2 was a 0-3 year-old child of Oceanian ancestry with RCM who died from rapidly progressive heart failure; in addition to the TNNT2 splice variant, a pathogenic variant in TNNI3 classified pathogenic as per ACMG guidelines was also identified. A total of 26 probands with a cardiac phenotype were reported (from clinical & research labs, ClinVar, and in Literature). Of these, 24 had a known cardiac phenotype, including 15 with HCM (including two diagnosed on autopsy following SCD), five with DCM (two presented at less than three years of age), three with sudden unexplained death, and one individual with high-burden premature ventricular contractions, syncope, and a family history of SCD. One individual lacked a specific diagnosis but had a family history of SCD, and in another, the diagnosis was not available. Four probands reported a family history of SCD in a close relative. Evidence of co-segregation with disease in families was reported for one family with HCM, with the variant identified in two affected relatives. At least four probands (15%) had an additional pathogenic variant that explained their cardiac phenotype. Ancestry was available for 22 probands, of which 21 probands were reported as having Oceanian ancestry, including Aotearoa New Zealand Māori, Samoan, Tongan, Polynesian, Pacific Islander, Australian Aboriginal and Torres Strait Islander, and Hawaiian. Among publicly available databases, TNNT2:c.571-1G>A (rs483352835) was present in gnomAD v4.0.0 in 13/780,762 (0.002%) alleles, with the highest sub-population frequencies among South Asian (5/74,486; 0.007%) and East Asian (1/41,260; 0.002%) alleles. Within Genome Asia 100K Project, the variant was present in 6/148 (4.1%) chromosomes in the Oceanian population, with a frequency of 2/4 (50%) chromosomes in the 2 Australian participants (one homozygote), and 4/140 (2.9%) in Papuan alleles. Among ancestry-relevant population sequencing data unavailable in the public domain, the variant was absent in the Taiwanese Biobank (0/3032; 0%). Within the Pacific Islands Rheumatic Heart Disease Genetics Network, the variant was present at a frequency of 0.088 (8.8%) within the Polynesian sub-group and 0.035 (3.5%) across the wider group, including Melanesians and South Asians. In a genome sequencing dataset (low-pass sequencing followed by imputation), of participants of Aotearoa New Zealand Māori and Pacific Islander ancestry recruited to a Health and Disability study, the variant was present at an allele frequency of 4.0% in East Polynesian individuals (n=139), and 3.6% among West Polynesian individuals (n=55). Based on the ACMG/AMP guidelines, which consider a minor allele frequency over 0.05 as benign (BA1 criterion), we classify the variant as benign. Given that 16 ClinVar assertions report this as a variant of uncertain significance, this classification downgrade will have a clinically meaningful impact. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Pathogenic	0.25
CADD	Pathogenic	32
DANN	Uncertain	0.99
Eigen	Pathogenic	0.97
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Uncertain	0.81	D
GERP RS		4.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.91
SpliceAI score (max)		0.31		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.31		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs483352835; hg19: chr1-201331523;