rs863225119

Positions:

• chr1-201359632-T-A
• chr1-201359632-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1 PM2 PP5 BP4

The NM_001276345.2(TNNT2):​c.842A>T​(p.Asn281Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000276 in 1,446,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000028 (0 hom.)
• Consequence: TNNT2 NM_001276345.2 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:4
• Conservation: PhyloP100: 1.93

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a chain Troponin T, cardiac muscle (size 296) in uniprot entity TNNT2_HUMAN there are 88 pathogenic changes around while only 9 benign (91%) in NM_001276345.2
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-201359632-T-A is Pathogenic according to our data. Variant chr1-201359632-T-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 217495.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=6, Uncertain_significance=4}. Variant chr1-201359632-T-A is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.39458075). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNNT2	NM_001276345.2	c.842A>T	p.Asn281Ile	missense_variant	16/17	ENST00000656932.1	NP_001263274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNNT2	ENST00000656932.1	c.842A>T	p.Asn281Ile	missense_variant	16/17		NM_001276345.2	ENSP00000499593	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000276 AC: 4 AN: 1446902 Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1 AN XY: 718144

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000462

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

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

Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 27, 2024	This sequence change replaces asparagine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 271 of the TNNT2 protein (p.Asn271Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hypertrophic cardiomyopathy (PMID: 12707239, 20038417, 22857948, 23396983; Invitae). This variant is also known as c.833A>T (p.Asn278Ile). ClinVar contains an entry for this variant (Variation ID: 217495). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TNNT2 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects TNNT2 function (PMID: 33025817). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Cardiomyopathy Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	All of Us Research Program, National Institutes of Health	May 31, 2023	This missense variant replaces asparagine with isoleucine at codon 271 of the TNNT2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that the variant may alter TNNT2 activity (PMID: 33025817). This variant has been reported in at least 4 individuals affected with hypertrophic cardiomyopathy (PMID: 12707239, 20038417, 22857948, 23396983). One of these individuals also carried a pathogenic variant in the MYH7 gene that could explain the observed phenotype (PMID: 23396983). This variant segregated with disease in multiple individuals in one family (PMID: 22857948). This variant has not been identified 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. -
Likely pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Mar 24, 2023	- -

not provided Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Sep 01, 2024	TNNT2: PM2, PS4:Moderate, PP1, PS3:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Dec 18, 2019	No data available from control populations to assess the frequency of this variant; however, this variant has not been detected at a significant frequency in presumably healthy individuals tested at GeneDx; Reported in ClinVar (ClinVar Variant ID# 217495; Landrum et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 33025817, 22857948, 12707239, 24093860) -

Dilated cardiomyopathy 1D Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Dec 22, 2022

ACMG classification criteria: PS3 supporting, PS4 moderated, PM2 moderated, PP1 supporting, BP4 supporting -

Hypertrophic cardiomyopathy 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory of Genetics and Molecular Cardiology, University of São Paulo

-

- -

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Aug 21, 2023

Variant summary: TNNT2 c.812A>T (p.Asn271Ile) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 227734 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.812A>T (also known as N268I) has been reported in the literature in individuals affected with hypertrophic cardiomyopathy and sudden death (examples: Richard_2003, Brito_2012, Lopes_2013, Marsiglia_2013, Halvorsen_2021). These data do not allow any conclusion about variant significance. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (example: Pettinato_2020). The following publications have been ascertained in the context of this evaluation (PMID: 22857948, 20038417, 34930847, 30297972, 23396983, 24093860, 33025817, 12707239). Five submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=2) and likely pathogenic (n=3). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 18, 2023

The p.N271I variant (also known as c.812A>T), located in coding exon 14 of the TNNT2 gene, results from an A to T substitution at nucleotide position 812. The asparagine at codon 271 is replaced by isoleucine, an amino acid with dissimilar properties. This variant has been detected in individuals with hypertrophic cardiomyopathy; however, in some cases, pathogenic variants in other cardiomyopathy-related genes were also detected, or gene analysis was limited to TNNT2 (Richard P et al. Circulation, 2003 May;107:2227-32; Gimeno JR et al. Rev Esp Cardiol, 2009 Dec;62:1473-7; Brito D et al. Rev Port Cardiol, 2012 Sep;31:577-87; Lopes LR et al. J Med Genet, 2013 Apr;50:228-39). A functional study has suggested that this variant may increase microtissue contraction; however, the physiological relevance of this finding is unclear (Pettinato AM et al. Circulation. 2020 Dec;142(23):2262-2275). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.85
CardioboostCm	Benign	0.092
BayesDel_addAF	Uncertain	0.020	T
BayesDel_noAF	Benign	-0.21
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.50	.;.;.;.;D;.;.;.;.;.;T
Eigen	Uncertain	0.20
Eigen_PC	Benign	0.22
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Uncertain	0.92	.;D;D;D;D;D;D;.;.;D;.
M_CAP	Uncertain	0.25	D
MetaRNN	Benign	0.39	T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.34	T
MutationAssessor	Benign	0.0	.;.;.;.;N;.;.;.;.;.;.
MutationTaster	Benign	0.99	D;D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.66	T
PROVEAN	Benign	-1.1	N;N;.;.;.;.;.;.;N;N;N
REVEL	Uncertain	0.38
Sift	Benign	0.41	T;T;.;.;.;.;.;.;T;T;T
Sift4G	Benign	0.41	T;T;T;T;T;T;T;T;T;T;.
Polyphen		0.98	.;.;.;.;D;.;.;.;.;.;.
Vest4		0.56
MutPred		0.41		.;.;.;.;Loss of disorder (P = 0.0144);.;.;.;.;.;.;
MVP		0.91
MPC		1.5
ClinPred		0.84	D
GERP RS		4.1
Varity_R		0.78
gMVP		0.60

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

Other links and lift over

dbSNP: rs863225119; hg19: chr1-201328760;