2-178526912-CT-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001267550.2(TTN):c.*99del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.016 ( 18 hom., cov: 0)
Exomes 𝑓: 0.023 ( 331 hom. )
Consequence
TTN
NM_001267550.2 3_prime_UTR
NM_001267550.2 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.858
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 2-178526912-CT-C is Benign according to our data. Variant chr2-178526912-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1204371.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-178526912-CT-C is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0161 (2453/152002) while in subpopulation NFE AF= 0.0229 (1557/67958). AF 95% confidence interval is 0.022. There are 18 homozygotes in gnomad4. There are 1230 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 18 AD,AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TTN | NM_001267550.2 | c.*99del | 3_prime_UTR_variant | 363/363 | ENST00000589042.5 | NP_001254479.2 | ||
TTN-AS1 | NR_038272.1 | n.219+3284del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TTN | ENST00000589042.5 | c.*99del | 3_prime_UTR_variant | 363/363 | 5 | NM_001267550.2 | ENSP00000467141 | P1 | ||
TTN-AS1 | ENST00000659121.1 | n.416+3284del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0162 AC: 2455AN: 151884Hom.: 18 Cov.: 0
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GnomAD4 exome AF: 0.0231 AC: 23720AN: 1025538Hom.: 331 Cov.: 13 AF XY: 0.0225 AC XY: 11315AN XY: 501946
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GnomAD4 genome AF: 0.0161 AC: 2453AN: 152002Hom.: 18 Cov.: 0 AF XY: 0.0166 AC XY: 1230AN XY: 74294
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at