chr2-178658787-T-A

Position:

chr2-178658787-T-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1

The NM_001267550.2(TTN):c.37461A>T(p.Glu12487Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.020 ( 2 hom., cov: 19)

Exomes 𝑓: 0.023 ( 96 hom. )

Failed GnomAD Quality Control

Consequence

TTN
NM_001267550.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -1.60

Variant links:

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]

TTN links:

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]

TTN-AS1 links:

LOC124906100 (HGNC:):

LOC124906100 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

PP2

Missense variant in gene, where missense usually causes diseases (based on misZ statistic), TTN. . Gene score misZ -1.1021 (greater than the threshold 3.09). Trascript score misZ 6.9794 (greater than threshold 3.09). GenCC has associacion of gene with dilated cardiomyopathy, tibial muscular dystrophy, early-onset myopathy with fatal cardiomyopathy, autosomal recessive centronuclear myopathy, hypertrophic cardiomyopathy, hypertrophic cardiomyopathy 9, TTN-related myopathy, dilated cardiomyopathy 1G, arrhythmogenic right ventricular cardiomyopathy, myopathy, myofibrillar, 9, with early respiratory failure, familial isolated dilated cardiomyopathy, childhood-onset progressive contractures-limb-girdle weakness-muscle dystrophy syndrome, autosomal recessive limb-girdle muscular dystrophy type 2J.

BP4

Computational evidence support a benign effect (MetaRNN=0.001691848).

BP6

Variant 2-178658787-T-A is Benign according to our data. Variant chr2-178658787-T-A is described in ClinVar as [Benign]. Clinvar id is 192213.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178658787-T-A is described in Lovd as [Benign]. Variant chr2-178658787-T-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TTN	NM_001267550.2 linkuse as main transcript	c.37461A>T	p.Glu12487Asp	missense_variant	183/363	ENST00000589042.5	NP_001254479.2
LOC124906100	XR_007087318.1 linkuse as main transcript	n.2185+14286T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TTN	ENST00000589042.5 linkuse as main transcript	c.37461A>T	p.Glu12487Asp	missense_variant	183/363	5	NM_001267550.2	ENSP00000467141	P1
TTN-AS1	ENST00000659121.1 linkuse as main transcript	n.502+61106T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0197

AC:

2899

AN:

147482

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00414

Gnomad AMI

AF:

0.0253

Gnomad AMR

AF:

0.0198

Gnomad ASJ

AF:

0.0171

Gnomad EAS

AF:

0.0730

Gnomad SAS

AF:

0.0243

Gnomad FIN

AF:

0.0394

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0220

Gnomad OTH

AF:

0.0188

GnomAD3 exomes

AF:

0.0268

AC:

6498

AN:

242278

Hom.:

AF XY:

0.0261

AC XY:

3445

AN XY:

131740

show subpopulations

Gnomad AFR exome

AF:

0.00416

Gnomad AMR exome

AF:

0.0285

Gnomad ASJ exome

AF:

0.0130

Gnomad EAS exome

AF:

0.0725

Gnomad SAS exome

AF:

0.0219

Gnomad FIN exome

AF:

0.0421

Gnomad NFE exome

AF:

0.0219

Gnomad OTH exome

AF:

0.0263

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0228

AC:

33001

AN:

1447754

Hom.:

Cov.:

AF XY:

0.0229

AC XY:

16523

AN XY:

720288

show subpopulations

Gnomad4 AFR exome

AF:

0.00402

Gnomad4 AMR exome

AF:

0.0283

Gnomad4 ASJ exome

AF:

0.0140

Gnomad4 EAS exome

AF:

0.0760

Gnomad4 SAS exome

AF:

0.0227

Gnomad4 FIN exome

AF:

0.0448

Gnomad4 NFE exome

AF:

0.0205

Gnomad4 OTH exome

AF:

0.0227

GnomAD4 genome

AF:

0.0196

AC:

2900

AN:

147606

Hom.:

Cov.:

AF XY:

0.0203

AC XY:

1460

AN XY:

71862

show subpopulations

Gnomad4 AFR

AF:

0.00413

Gnomad4 AMR

AF:

0.0197

Gnomad4 ASJ

AF:

0.0171

Gnomad4 EAS

AF:

0.0734

Gnomad4 SAS

AF:

0.0243

Gnomad4 FIN

AF:

0.0394

Gnomad4 NFE

AF:

0.0220

Gnomad4 OTH

AF:

0.0186

Alfa

AF:

0.0198

Hom.:

ESP6500AA

AF:

0.00514

AC:

ESP6500EA

AF:

0.0151

AC:

ExAC

AF:

0.0303

AC:

3648

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Dec 18, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

not specified

Benign:2

Benign, criteria provided, single submitter	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jun 24, 2013	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

Autosomal recessive limb-girdle muscular dystrophy type 2J

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

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

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 24, 2024

- -

Early-onset myopathy with fatal cardiomyopathy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Myopathy, myofibrillar, 9, with early respiratory failure

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Tibial muscular dystrophy

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 10, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.55

BayesDel_noAF

Benign

-0.54

CADD

Benign

6.9

DANN

Benign

0.87

Eigen

Benign

-0.70

Eigen_PC

Benign

-0.81

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.27

T;.

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.90

D;D;D;D;N;N

Vest4

0.099

MPC

0.13

ClinPred

0.0053

GERP RS

-1.0

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

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