chr1-201369850-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001276345.2(TNNT2):c.68-5C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00178 in 1,614,188 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001276345.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00187 AC: 285AN: 152212Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00387 AC: 972AN: 251422Hom.: 21 AF XY: 0.00386 AC XY: 525AN XY: 135900
GnomAD4 exome AF: 0.00177 AC: 2592AN: 1461858Hom.: 45 Cov.: 35 AF XY: 0.00178 AC XY: 1295AN XY: 727234
GnomAD4 genome AF: 0.00186 AC: 284AN: 152330Hom.: 7 Cov.: 33 AF XY: 0.00215 AC XY: 160AN XY: 74496
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Dilated cardiomyopathy 1D Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Primary dilated cardiomyopathy;C0007194:Hypertrophic cardiomyopathy;C0520806:Sudden unexplained death Benign:1
Benign, criteria provided, single submitter | research | Agnes Ginges Centre for Molecular Cardiology, Centenary Institute | Oct 12, 2018 | TNNT2 c.68-5C>T was identified in a HCM, DCM and sudden unexplained death proband, however it is very common in population databases such as the Genome Aggregation Database (AF=0.0036; http://gnomad.broadinstitute.org/), therefore we classify this variant as 'benign'. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 23, 2023 | - - |
Cardiomyopathy, familial restrictive, 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Hypertrophic cardiomyopathy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Apr 11, 2023 | - - |
Dilated cardiomyopathy 1D;C1861864:Hypertrophic cardiomyopathy 2;C2676271:Cardiomyopathy, familial restrictive, 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 08, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at