2-178752043-GAAAAA-GAAAAAAA

Variant names:

• chr2-178752043-G-GAA
• rs58651353
• NM_001267550.2:c.11311+1079_11311+1080dupTT

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP6

The NM_001267550.2(TTN):​c.11311+1079_11311+1080dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.000028 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00042 (0 hom.)
• Consequence: TTN NM_001267550.2 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 2.56
• Publications: 5 publications found

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-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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP6: Variant 2-178752043-G-GAA is Benign according to our data. Variant chr2-178752043-G-GAA is described in ClinVar as Likely_benign. ClinVar VariationId is 3045594.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTN	NM_001267550.2	c.11311+1079_11311+1080dupTT		intron_variant	Intron 47 of 362	ENST00000589042.5	NP_001254479.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TTN	ENST00000589042.5	c.11311+1080_11311+1081insTT		intron_variant	Intron 47 of 362	5	NM_001267550.2	ENSP00000467141.1

Frequencies

GnomAD3 genomes AF: 0.0000284 AC: 4 AN: 140932 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000261

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000120

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000310

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.000788 AC: 128 AN: 162534 AF XY: 0.000796

Gnomad AFR exome AF: 0.00231

Gnomad AMR exome AF: 0.00105

Gnomad ASJ exome AF: 0.00283

Gnomad EAS exome AF: 0.0000897

Gnomad FIN exome AF: 0.000139

Gnomad NFE exome AF: 0.000636

Gnomad OTH exome AF: 0.00132

GnomAD4 exome AF: 0.000423 AC: 532 AN: 1256932 Hom.: 0 Cov.: 0 AF XY: 0.000397 AC XY: 250 AN XY: 629250

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00175 AC: 46 AN: 26358

American (AMR) AF: 0.000963 AC: 31 AN: 32186

Ashkenazi Jewish (ASJ) AF: 0.00236 AC: 54 AN: 22896

East Asian (EAS) AF: 0.0000575 AC: 2 AN: 34794

South Asian (SAS) AF: 0.000691 AC: 50 AN: 72326

European-Finnish (FIN) AF: 0.0000900 AC: 4 AN: 44424

Middle Eastern (MID) AF: 0.000601 AC: 3 AN: 4994

European-Non Finnish (NFE) AF: 0.000325 AC: 314 AN: 966680

Other (OTH) AF: 0.000536 AC: 28 AN: 52274

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0000284 AC: 4 AN: 140986 Hom.: 0 Cov.: 0 AF XY: 0.0000293 AC XY: 2 AN XY: 68252

African (AFR) AF: 0.0000260 AC: 1 AN: 38416

American (AMR) AF: 0.00 AC: 0 AN: 14048

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3308

East Asian (EAS) AF: 0.00 AC: 0 AN: 4874

South Asian (SAS) AF: 0.00 AC: 0 AN: 4464

European-Finnish (FIN) AF: 0.000120 AC: 1 AN: 8348

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 278

European-Non Finnish (NFE) AF: 0.0000310 AC: 2 AN: 64438

Other (OTH) AF: 0.00 AC: 0 AN: 1932

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

TTN-related disorder Benign:1

Oct 21, 2019

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.6
Mutation Taster		=99/1	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs58651353; hg19: chr2-179616770;