rs202234172

chr2-178689897-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Moderate PP3_Strong

The NM_001267550.2(TTN):c.31763-1G>A variant causes a splice acceptor change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000523 in 1,612,568 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00045 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00053 (0 hom.)
• Consequence: TTN NM_001267550.2 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:9 B:2
• Conservation: PhyloP100: 3.57

Genes affected

TTN (HGNC:12403): (titin) This gene encodes a large abundant protein of striated muscle. The product of this gene is divided into two regions, a N-terminal I-band and a C-terminal A-band. The I-band, which is the elastic part of the molecule, contains two regions of tandem immunoglobulin domains on either side of a PEVK region that is rich in proline, glutamate, valine and lysine. The A-band, which is thought to act as a protein-ruler, contains a mixture of immunoglobulin and fibronectin repeats, and possesses kinase activity. An N-terminal Z-disc region and a C-terminal M-line region bind to the Z-line and M-line of the sarcomere, respectively, so that a single titin molecule spans half the length of a sarcomere. Titin also contains binding sites for muscle associated proteins so it serves as an adhesion template for the assembly of contractile machinery in muscle cells. It has also been identified as a structural protein for chromosomes. Alternative splicing of this gene results in multiple transcript variants. Considerable variability exists in the I-band, the M-line and the Z-disc regions of titin. Variability in the I-band region contributes to the differences in elasticity of different titin isoforms and, therefore, to the differences in elasticity of different muscle types. Mutations in this gene are associated with familial hypertrophic cardiomyopathy 9, and autoantibodies to titin are produced in patients with the autoimmune disease scleroderma. [provided by RefSeq, Feb 2012]

LOC124907912 (HGNC:):

TTN-AS1 (HGNC:44124): (TTN antisense RNA 1) This gene encodes a non-coding RNA transcribed from the opposite strand to the titin gene. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 7.686893E-4 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.6, offset of 6, new splice context is: tcaaaaactttaaatcccAGagg. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. No scorers claiming Benign.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TTN	NM_001267550.2	c.31763-1G>A		splice_acceptor_variant		ENST00000589042.5
LOC124907912	XR_007087321.1	n.1760C>T		non_coding_transcript_exon_variant	1/2
LOC124906100	XR_007087318.1	n.2186-23857C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TTN	ENST00000589042.5	c.31763-1G>A		splice_acceptor_variant		5	NM_001267550.2	P1
TTN-AS1	ENST00000659121.1	n.503-44607C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.000447 AC: 68 AN: 152092 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

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: 0.000867

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000338 AC: 84 AN: 248510 Hom.: 0 AF XY: 0.000252 AC XY: 34 AN XY: 134780

Gnomad AFR exome AF: 0.000129

Gnomad AMR exome AF: 0.000116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000683

Gnomad OTH exome AF: 0.000166

GnomAD4 exome AF: 0.000531 AC: 776 AN: 1460476 Hom.: 0 Cov.: 31 AF XY: 0.000497 AC XY: 361 AN XY: 726510

Gnomad4 AFR exome AF: 0.0000898

Gnomad4 AMR exome AF: 0.000135

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000674

Gnomad4 OTH exome AF: 0.000282

GnomAD4 genome AF: 0.000447 AC: 68 AN: 152092 Hom.: 0 Cov.: 32 AF XY: 0.000377 AC XY: 28 AN XY: 74314

Gnomad4 AFR AF: 0.000145

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000867

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000633 Hom.: 0

Bravo AF: 0.000397

TwinsUK AF: 0.000809 AC: 3

ALSPAC AF: 0.00130 AC: 5

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000613 AC: 5

ExAC AF: 0.000273 AC: 33

EpiCase AF: 0.000710

EpiControl AF: 0.000296

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:9 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 01, 2016	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Aug 04, 2021	Reported in individuals with hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), and peripartum cardiomyopathy (Lopes et al., 2013; Roberts et al., 2015; Ware et al., 2016; Minoche et al., 2019); also described as c.28031-1 G>A, c.31763-1G>A, and g.179554624 C>T due to the use of alternate transcripts and/or nomenclature; Reported in ClinVar (ClinVar Variant ID# 46855; Landrum et al., 2016); Canonical splice site variant located in the I-band region that does not affect one of the constitutive exons; studies suggest that truncating variants affecting constitutive exons throughout the TTN gene are significantly associated with DCM (Deo, 2016; Schafer et al., 2017); This variant is associated with the following publications: (PMID: 26735901, 23396983, 25589632, 26777568, 24980681, 29961767, 30724488) -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Nov 22, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2017	- -

not specified Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 23, 2023	Variant summary: TTN c.28031-1G>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. One computational tool predicts the variant abolishes a 3 acceptor site and two predict the variant creates a cryptic exonic one. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00034 in 248510 control chromosomes, predominantly at a frequency of 0.00068 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 2-fold of the estimated maximal expected allele frequency for a pathogenic variant in TTN causing Dilated Cardiomyopathy phenotype (0.00039), suggesting that the variant may be a benign polymorphism found primarily in populations of Non-Finnish European origin. c.28031-1G>A has been reported in the literature in individuals affected with hypertrophic cardiomyopathy, dilated cardiomyopathy, peripartum cardiomyopathy, atrial fibrillation, ventricular arrhythmia, heart failure, mitral valve disease, and supraventricular tachycardia (Lopes_2013, Roberts_2015, Ware_2016, Jansweijer_2017, Choi_2018, Verhagen_2018, Minoche_2019, Choi_2020, Goli_2021, Vissing_2021, Jurgens_2022), but it was also detected in multiple controls (Choi_2018, Choi_2020, Jurgens_2022). In at least one of the studies the variant was found to incompletely segregate with disease in affected members of one family (Minoche_2019). These reports do not provide unequivocal conclusions about association of the variant with Dilated Cardiomyopathy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance, two ClinVar submitters (evaluation after 2014) cite it as likely benign, and one ClinVar submitter (evaluation after 2014) cites it as likely pathogenic. The variant is located within the I-band region of titin, adjacent to a symmetrical exon that is not constitutively expressed. Heterozygous mutations that truncate full-length titin (TTNtv, titin truncating variants) are the most common genetic cause for severe and familial dilated cardiomyopathy (DCM). Nevertheless, TTNtv also occur in approximately 2% of individuals without overt cardiomyopathy. Importantly, TTNtv associated with DCM are predominantly located in the A-band region (PMID 22335739, 25589632). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 06, 2018	Variant classified as Uncertain Significance - Favor Benign. The c.28031-1G>A va riant in TTN has been reported in at least 1 individual with peripartum cardiomy opathy, 2 individuals with DCM, and 1 individual with interventricular conductio n delay (Ware 2016, Roberts 2015, Akinrinade 2016, LMM data). This variant has a lso been identified in 0.07% (83/126420) of European chromosomes by the Genome A ggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs202234172 ), which reduces the likelihood that the variant causes disease. This variant oc curs in the invariant region (+/- 1,2) of the splice consensus sequence and is p redicted to cause altered splicing leading to an abnormal or absent protein. Tru ncating variants in TTN are strongly associated with DCM, if they impact the exo ns encoding for the A-band (Herman 2012, Pugh 2014) and/or are located in an exo n that is highly expressed in the heart (Roberts 2015). Variants in the I-band, where the c.28031-1G>A variant is located, are less likely to be disease causing (Pugh 2014, Roberts 2015). In summary, while the clinical significance of the c .28031-1G>A variant is uncertain, its frequency suggests that it is more likely to be benign. ACMG/AMP Criteria applied: PS4_Supporting; BS1. -
Uncertain significance, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 06, 2016	- -

Primary dilated cardiomyopathy Pathogenic:1 Uncertain:1

Likely pathogenic, criteria provided, single submitter	research	Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	Oct 08, 2014	This TTN truncating variant (TTNtv) was identified in one individual in this cohort and is located in an exon with intermediate levels of cardiac expression. In the seven cohorts assessed, TTNtv were found in 14% of ambulant DCM, 22% end-stage or familial DCM, and 2% controls. Heterozygous nonsense, frameshift and canonical splice-disrupting variants found in constitutive and other highly utilised exons are highly likely to be pathogenic when identified in individuals with phenotypically confirmed DCM. TTNtv found incidentally in healthy individuals (excluding familial assessment of DCM relatives) are thought to have low penetrance, particularly when identified in exons that are not constitutively expressed in the heart. -
Uncertain significance, criteria provided, single submitter	research	Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	Oct 08, 2014	This TTN truncating variant (TTNtv) was identified in one individual in this cohort and is located in an exon with intermediate levels of cardiac expression. In the seven cohorts assessed, TTNtv were found in 14% of ambulant DCM, 22% end-stage or familial DCM, and 2% controls. Heterozygous nonsense, frameshift and canonical splice-disrupting variants found in constitutive and other highly utilised exons are highly likely to be pathogenic when identified in individuals with phenotypically confirmed DCM. TTNtv found incidentally in healthy individuals (excluding familial assessment of DCM relatives) are thought to have low penetrance, particularly when identified in exons that are not constitutively expressed in the heart. -

Tip-toe gait Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino

Nov 24, 2021

- -

Dilated cardiomyopathy 1G Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Zotz-Klimas Genetics Lab, MVZ Zotz Klimas

Oct 09, 2023

- -

Autosomal recessive limb-girdle muscular dystrophy type 2J;C1858763:Dilated cardiomyopathy 1G Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Jan 17, 2024

- -

Cardiomyopathy Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

May 06, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Uncertain	0.073	D
BayesDel_noAF	Pathogenic	0.29
Cadd	Pathogenic	34
Dann	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.85
FATHMM_MKL	Uncertain	0.89	D
MutationTaster	Benign	1.0	D;D;D;D;D;D
GERP RS		5.3

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.86
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.88		Position offset: -7
DS_AL_spliceai		1.0		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: rs202234172; hg19: chr2-179554624;