chr1-201359220-C-T

Position:

chr1-201359220-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 4P and 6B. PM1PM5BP4_ModerateBS2

The NM_001276345.2(TNNT2):c.887G>A(p.Arg296His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000286 in 1,610,148 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 Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R296C) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000027 ( 0 hom. )

Consequence

TNNT2
NM_001276345.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts P:1U:15

Conservation

PhyloP100: 1.79

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 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

PM5

Other missense variant is known to change same aminoacid residue: Variant chr1-201359221-G-A is described in Lovd as [Likely_pathogenic].

BP4

Computational evidence support a benign effect (MetaRNN=0.14857218).

BS2

High AC in GnomAd4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNNT2	NM_001276345.2 linkuse as main transcript	c.887G>A	p.Arg296His	missense_variant	17/17	ENST00000656932.1	NP_001263274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNNT2	ENST00000656932.1 linkuse as main transcript	c.887G>A	p.Arg296His	missense_variant	17/17		NM_001276345.2	ENSP00000499593	A2	P45379-1

Frequencies

GnomAD3 genomes

AF:

0.0000460

AC:

AN:

152158

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000618

AC:

AN:

242560

Hom.:

AF XY:

0.0000688

AC XY:

AN XY:

130782

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000779

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000910

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000267

AC:

AN:

1457990

Hom.:

Cov.:

AF XY:

0.0000290

AC XY:

AN XY:

724628

show subpopulations

Gnomad4 AFR exome

AF:

0.0000598

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.000353

Gnomad4 SAS exome

AF:

0.0000118

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000189

Gnomad4 OTH exome

AF:

0.0000166

GnomAD4 genome

AF:

0.0000460

AC:

AN:

152158

Hom.:

Cov.:

AF XY:

0.0000673

AC XY:

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000963

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000537

Hom.:

Bravo

AF:

0.0000378

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.0000659

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1Uncertain:15

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Blueprint Genetics	Nov 22, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Apr 18, 2024	Published functional studies are contradictory as to whether this variant significantly affects protein function (PMID: 32815737, 33025817); Although instances of segregation with disease have been reported, this variant has also been observed in several unaffected family members in published literature and at GeneDx (PMID: 25086479, 26507537); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24111713, 18761664, 23785128, 25524337, 12707239, 25351510, 7898523, 23711808, 23299917, 25637381, 15519027, 12860912, 22321274, 26507537, 20031601, 28138913, 27532257, 28771489, 15958377, 29121657, 30165862, 33025817, 28356264, Kassem2017[CaseReport], 32815737, 35216312, AlloubaM2022[Preprint], 34127679, 37107598, 37652022, 37377076, 37431535, 25086479, 27082122, 19035361) -
Uncertain significance, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Jan 28, 2016	p.Arg286His (c.857 G>A) in TNNT2 (NM_001001430.1) We re-reviewed this variant on September 2nd, 2014 and again on January 21st, 2015. This variant is difficulty to parse without current understanding of the genome and the genetic basis of HCM. It is more common in Asian individuals unselected for HCM than we would expect for a pathogenic HCM variant. However, there are many cases, suggesting it may be enriched in cases. Notably, there are many non-Asian cases. Given these data, it seems likely that the variant is contributing to HCM in the patient and these other cases. It maybe a modifier or susceptibility factor However, it may not be the primary driver. Until we can better understand the role of variants like this we will consider it a variant of uncertain significance. This variant has been reported in at least 13 unrelated probands with HCM, in addition to this patient. Unfortunately several of this cases are unpublished. Also most of those cases don't have ancestry data available and the majority that do are Asian, like the patient. There is no segregation data on this variant. We have seen this variant one other Asian family with HCM in our center. Van Driest et al (2003) first reported this variant in two unrelated probands with HCM in their American cohort (ancestry not reported). The same group later reported an individual with HCM who had this variant and a variant in MYBPC3, p.Ala833Thr (Van Driest et al 2004). Unfortunately it is unclear if that case is the same as one of the previously reported cases. Andersen et al (2008 (2009 on pubmed)) reported the variant in two unrelated probands with HCM in their Dutch cohort. Ancestry was not reported. Ripoll-Vera et al (2015) reported a total of 5 families with HCM with this variant in their Spanish cohort. This was out of 180 families with hereditary cardiomyopathies, most of them having HCM (total number with HCM not specified). Probands underwent sequencing of MYBPC3, MYH7, TNNT2, TNNI3, and TPM1, One family with this variant also carried Arg326Gln in MYBPC3, which is in ClinVar with an assertion of likely benign or benign by 7 different groups (all concordant). In addition to the proband, three unaffected relatives in three different families carried p.Arg286His. It appears that no affected relatives had genetic testing. They noted a founder effect for one other variant observed in their cohort but did not report whether they assessed possible founder effect for p.Arg286His. Ancestry is not reported, however the cases were ascertained at a hospital in the Balearic Islands, Spain. This report is presumably redundant with their abstract from the 2011 European Society of Cardiology meeting and a thesis available online by Tomas Ripoll Vera). Yang et al (2011) observed the variant in 1 of 100 individuals with HCM in their Chinese cohort (article is in Chinese but an English abstract was reviewed). This is very likely the same case reported in an abstract from the 2011 Annual Congress of the European Cardiac Arrhythmia Society by what appears to be the same group (Wenling et al). The arginine at codon 286 is conserved across species. This is a conservative amino acid change with a polar Arginine replaced with a polar Histidine. In silico analysis with Polyphen predicts the variant to be probably damaging. Another variant at the same codon has been reported in association with HCM (p.Arg286Cys; Richard et al 2003, Miliou et al 2005; no segregation data). Two variants at codon 278 have also been reported in HCM cases (p.Arg278Pro, p.Arg278Cys). The variant was reported online in 7 of 44405 individuals in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of January 20th, 2015). Specifically, the variant was observed in 7 of 3196 East Asian individuals (MAF 0.0009387). It was also seen in one European. The phenotype of tho -
Uncertain significance, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -

Cardiomyopathy

Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 26, 2022	This missense variant replaces arginine with histidine at codon 286 of the TNNT2 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies using induced pluripotent stem cells provide some evidence that this variant may impact TNNT2 function (PMID: 32815737). This variant has been reported in multiple individuals and families affected with hypertrophic cardiomyopathy (PMID: 12860912, 19035361, 23711808, 24111713, 25086479, 25351510, 26507537, 27082122, 27532257, 28356264, 28771489, 32815737). Compound heterozygous individuals showed a more severe phenotype than heterozygous individuals (PMID: 25086479). Family studies are inconclusive as to whether this variant segregates with hypertrophic cardiomyopathy or not (PMID: 19035361, 25086479, 26507537). This variant has been identified in healthy control cohorts, and is estimated to have a low penetrance (PMID: 32815737). This variant has been identified in 19/273936 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this is a variant with unknown functional impact that has been reported in multiple individuals affected with hypertrophic cardiomyopathy. However, this variant also occurs at an appreciable frequency in the general population and it is inconclusive whether this variant segregates with disease in affected families. Additional studies are necessary 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	Oct 30, 2023	This missense variant replaces arginine with histidine at codon 286 of the TNNT2 protein. Computational prediction tools indicate that this variant's impact on protein structure and function is inconclusive. Functional studies using induced pluripotent stem cells provide some evidence that this variant may impact TNNT2 function (PMID: 32815737). This variant has been reported in multiple individuals and families affected with hypertrophic cardiomyopathy (PMID: 12860912, 19035361, 23711808, 24111713, 25086479, 25351510, 26507537, 27082122, 27532257, 28356264, 28771489, 32815737, 33495596, 33495597, 37107598). Some of these individuals also carried pathogenic variants in other genes associated with hypertrophic cardiomyopathy (PMID: 25086479 , 37107598). Compound heterozygous individuals showed a more severe phenotype than heterozygous individuals (PMID: 25086479). Family studies are inconclusive as to whether this variant segregates with hypertrophic cardiomyopathy or not (PMID: 19035361, 25086479, 26507537). This variant has been identified in healthy control cohorts, and is estimated to have a low penetrance (PMID: 32815737). This variant has been identified in 19/273936 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this is a variant with unknown functional impact that has been reported in multiple individuals affected with hypertrophic cardiomyopathy. However, this variant also occurs at an appreciable frequency in the general population and it is inconclusive whether this variant segregates with disease in affected families. Additional studies are necessary 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	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	May 26, 2023	- -

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 17, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 286 of the TNNT2 protein (p.Arg286His). This variant is present in population databases (rs141121678, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 12860912, 23711808, 25086479, 26507537, 27082122, 28356264). ClinVar contains an entry for this variant (Variation ID: 43677). 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 95%. Experimental studies have shown that this missense change affects TNNT2 function (PMID: 32815737). 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. -

Primary familial hypertrophic cardiomyopathy

Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

CSER _CC_NCGL, University of Washington

Jun 01, 2014

- -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jul 16, 2018

Variant classified as Uncertain Significance - Favor Benign. The p.Arg286His var iant in TNNT2 has been reported in >13 individuals with HCM and segregated with disease in at least 1 affected relative (Van Driest 2003, Van Driest 2004, Ande rsen 2009, Zhao 2016, Ripoll-Vera 2016, Viswanathan 2017). This variant has been identified in 0.09% (16/18472) of East Asian chromosomes by the Genome Aggregat ion Database (gnomAD, http://gnomad.broadinstitute.org/) and is reported in Clin Var (Variation ID: 43677). Computational prediction tools and conservation analy sis suggest that the p.Arg286His variant may impact the protein, though this inf ormation is not predictive enough to determine pathogenicity. In summary, while the clinical significance of the p.Arg286His variant is uncertain, its frequency suggests that it is more likely to be benign. ACMG/AMP Criteria applied: PS4, P P3, BS1. -

Dilated cardiomyopathy 1D

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Apr 11, 2023

- -

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

Mar 12, 2024

The p.R286H variant (also known as c.857G>A), located in coding exon 15 of the TNNT2 gene, results from a G to A substitution at nucleotide position 857. The arginine at codon 286 is replaced by histidine, an amino acid with highly similar properties. This variant has been detected in numerous individuals with hypertrophic cardiomyopathy (HCM); however, it has also been reported in control cohorts, and some HCM cases had additional cardiac variants detected (Van Driest SL et al., Circulation 2003 Jul; 108(4):445-51; Andersen PS et al., Hum. Mutat. 2009 Mar; 30(3):363-70; Berge KE et al., Clin. Genet. 2014 Oct; 86(4):355-60; Chiou KR et al., J Cardiol 2015 Mar; 65(3):250-6; Lopes LR et al., Heart 2015 Feb; 101(4):294-301; Ripoll-Vera T et al., Rev Esp Cardiol (Engl Ed) 2016 Feb; 69(2):149-58; Pua CJ et al. Circ Genom Precis Med, 2020 10;13:424-434). Limited studies in iPSC-CMs suggest this variant may have some functional impact (Pua CJ et al. Circ Genom Precis Med, 2020 10;13:424-434). Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.78

CardioboostCm

Uncertain

0.20

BayesDel_addAF

Benign

-0.0037

BayesDel_noAF

Pathogenic

0.14

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.61

.;.;.;.;D;.;.;.;.;.

Eigen

Uncertain

0.63

Eigen_PC

Uncertain

0.55

FATHMM_MKL

Uncertain

0.96

LIST_S2

Uncertain

0.88

.;D;D;D;D;D;D;.;.;D

M_CAP

Uncertain

0.24

MetaRNN

Benign

0.15

T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Uncertain

2.6

.;.;.;.;M;.;.;.;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D;D;D;D;D

PrimateAI

Uncertain

0.70

PROVEAN

Uncertain

-2.7

D;D;.;.;.;D;.;.;D;D

REVEL

Uncertain

0.55

Sift

Pathogenic

0.0

D;D;.;.;.;D;.;.;D;D

Sift4G

Uncertain

0.0020

D;D;D;D;D;D;D;D;D;D

Polyphen

1.0

.;.;.;.;D;.;.;.;.;.

Vest4

0.49

MVP

0.95

MPC

1.6

ClinPred

0.54

GERP RS

4.0

Varity_R

0.12

gMVP

0.39

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over