rs6715406

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001267550.2(TTN):​c.2244G>A​(p.Glu748=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 1,613,814 control chromosomes in the GnomAD database, including 116,401 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8777 hom., cov: 31)
Exomes 𝑓: 0.37 ( 107624 hom. )

Consequence

TTN
NM_001267550.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:21

Conservation

PhyloP100: 2.15
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
Variant 2-178785974-C-T is Benign according to our data. Variant chr2-178785974-C-T is described in ClinVar as [Benign]. Clinvar id is 46774.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-178785974-C-T is described in Lovd as [Benign]. Variant chr2-178785974-C-T is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=2.15 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TTNNM_001267550.2 linkuse as main transcriptc.2244G>A p.Glu748= synonymous_variant 14/363 ENST00000589042.5
TTNNM_133379.5 linkuse as main transcriptc.2244G>A p.Glu748= synonymous_variant 14/46 ENST00000360870.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TTNENST00000589042.5 linkuse as main transcriptc.2244G>A p.Glu748= synonymous_variant 14/3635 NM_001267550.2 P1
TTNENST00000360870.10 linkuse as main transcriptc.2244G>A p.Glu748= synonymous_variant 14/465 NM_133379.5 Q8WZ42-6

Frequencies

GnomAD3 genomes
AF:
0.320
AC:
48659
AN:
151868
Hom.:
8780
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.194
Gnomad AMI
AF:
0.563
Gnomad AMR
AF:
0.245
Gnomad ASJ
AF:
0.336
Gnomad EAS
AF:
0.0816
Gnomad SAS
AF:
0.251
Gnomad FIN
AF:
0.475
Gnomad MID
AF:
0.414
Gnomad NFE
AF:
0.409
Gnomad OTH
AF:
0.317
GnomAD3 exomes
AF:
0.316
AC:
79397
AN:
251086
Hom.:
14492
AF XY:
0.323
AC XY:
43764
AN XY:
135682
show subpopulations
Gnomad AFR exome
AF:
0.192
Gnomad AMR exome
AF:
0.170
Gnomad ASJ exome
AF:
0.329
Gnomad EAS exome
AF:
0.0729
Gnomad SAS exome
AF:
0.254
Gnomad FIN exome
AF:
0.470
Gnomad NFE exome
AF:
0.403
Gnomad OTH exome
AF:
0.334
GnomAD4 exome
AF:
0.374
AC:
547035
AN:
1461828
Hom.:
107624
Cov.:
70
AF XY:
0.372
AC XY:
270315
AN XY:
727220
show subpopulations
Gnomad4 AFR exome
AF:
0.189
Gnomad4 AMR exome
AF:
0.178
Gnomad4 ASJ exome
AF:
0.328
Gnomad4 EAS exome
AF:
0.0662
Gnomad4 SAS exome
AF:
0.256
Gnomad4 FIN exome
AF:
0.462
Gnomad4 NFE exome
AF:
0.406
Gnomad4 OTH exome
AF:
0.346
GnomAD4 genome
AF:
0.320
AC:
48653
AN:
151986
Hom.:
8777
Cov.:
31
AF XY:
0.317
AC XY:
23520
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.193
Gnomad4 AMR
AF:
0.244
Gnomad4 ASJ
AF:
0.336
Gnomad4 EAS
AF:
0.0816
Gnomad4 SAS
AF:
0.251
Gnomad4 FIN
AF:
0.475
Gnomad4 NFE
AF:
0.409
Gnomad4 OTH
AF:
0.315
Alfa
AF:
0.377
Hom.:
14985
Bravo
AF:
0.294
Asia WGS
AF:
0.152
AC:
530
AN:
3478
EpiCase
AF:
0.396
EpiControl
AF:
0.392

ClinVar

Significance: Benign
Submissions summary: Benign:21
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:8
Benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineSep 16, 2011- -
Benign, criteria provided, single submitterclinical testingGeneDxOct 30, 2012This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoAug 15, 2013- -
Benign, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpAug 09, 2019- -
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Autosomal recessive limb-girdle muscular dystrophy type 2J Benign:2
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 10, 2021- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Early-onset myopathy with fatal cardiomyopathy Benign:2
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 10, 2021- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsNov 02, 2018- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Tibial muscular dystrophy Benign:2
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 10, 2021- -
Myopathy, myofibrillar, 9, with early respiratory failure Benign:2
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 10, 2021- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Autosomal recessive limb-girdle muscular dystrophy type 2J;C1858763:Dilated cardiomyopathy 1G Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Dilated cardiomyopathy 1G Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 12, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitterclinical testingAmbry GeneticsFeb 07, 2019This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.35
CADD
Benign
13
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.060
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.

Other links and lift over

dbSNP: rs6715406; hg19: chr2-179650701; COSMIC: COSV59948304; COSMIC: COSV59948304; API