chr1-201364336-G-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001276345.2(TNNT2):c.451C>A(p.Arg151Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000713 in 1,613,006 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R151R) has been classified as Likely benign.
Frequency
Consequence
NM_001276345.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152202Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000116 AC: 29AN: 250116Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135360
GnomAD4 exome AF: 0.0000712 AC: 104AN: 1460686Hom.: 2 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 726662
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152320Hom.: 1 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74492
ClinVar
Submissions by phenotype
Cardiomyopathy Benign:2
- -
- -
Dilated cardiomyopathy 1D;C1861864:Hypertrophic cardiomyopathy 2;C2676271:Cardiomyopathy, familial restrictive, 3 Benign:2
- -
- -
not specified Benign:1
Arg141Arg in exon 10 of TNNT2: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. Arg141Arg in exon 10 of TNNT2 (allele freque ncy = n/a) -
Dilated cardiomyopathy 1D Benign:1
- -
not provided Benign:1
- -
Cardiomyopathy, familial restrictive, 3 Benign:1
- -
Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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. -
Hypertrophic cardiomyopathy 2 Benign:1
- -
TNNT2-related disorder Benign:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at