Submissions for variant NM_001267550.2(TTN):c.11254+1G>C

Total submissions: 2

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV004787157	SCV005398809	uncertain significance	Early-onset myopathy with fatal cardiomyopathy	2024-09-19	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3B. Following criteria are met: 0102 - Loss of function is known mechanism of disease in this gene. In addition, dominant-negative is also a suggested mechanism. (PMID: 25589632). (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM). (I) 0112 - The condition associated with this gene has incomplete penetrance. Variants in this gene that result in a premature termination codon (PTC) are known to have reduced penetrance in DCM (PMID: 25589632). (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0219 - This variant is non-coding in an alternative transcript. This variant is only coding in the Meta-transcript NM_001267550.1 and NM_133437.4, but is not coding in the cardiac (NM_003319.4) or skeletal muscle (NM_133378.4) transcripts. However recent literature has shown an association between variants only coding in the Meta-transcript and autosomal recessive congenital titinopathy (PMID: 32778822). (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v3) <0.01 for a recessive condition (10 heterozygote, 0 homozygotes). (SP) 0311 - An alternative nucleotide changes at the same canonical splice site is present in gnomAD (v3) (201 heterozygotes, 1 homozygote). (I) 0506 - Abnormal splicing is not predicted and nucleotide is poorly conserved. (SB) 0710 - Another canonical splice variant comparable to the one identified in this case has inconclusive previous evidence for pathogenicity. c.11254+2T>C has been classified as benign, likely benign and a VUS by clinical laboratories in ClinVar. (I) 0803 - This variant has limited previous evidence of pathogenicity in an unrelated individual. This variant has been classified as likely pathogenic in an individual with dilated cardiomyopathy (PMID: 37461109). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
PreventionGenetics, part of Exact Sciences	RCV004735004	SCV005344508	uncertain significance	TTN-related disorder	2024-09-06	no assertion criteria provided	clinical testing	The TTN c.11254+1G>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported as an incidental truncating variant finding using another transcript (c.10741+1G>C, NM_133437) in a patient from an exome sequencing cohort (Supplemental Table 1, Connell et al. 2021. PubMed ID:33226272). This variant is reported in 0.021% of alleles in individuals of East Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.