1-201362426-T-G
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001276345.2(TNNT2):c.601-32A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 1,611,296 control chromosomes in the GnomAD database, including 422,566 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.74 ( 41807 hom., cov: 32)
Exomes 𝑓: 0.72 ( 380759 hom. )
Consequence
TNNT2
NM_001276345.2 intron
NM_001276345.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.21
Genes affected
TNNT2 (HGNC:11949): (troponin T2, cardiac type) This gene encodes the cardiac isoform of troponin T. The encoded protein is the tropomyosin-binding subunit of the troponin complex, which is located on the thin filament of striated muscles and regulates muscle contraction in response to alterations in intracellular calcium ion concentration. Mutations in this gene have been associated with familial hypertrophic cardiomyopathy as well as with dilated cardiomyopathy. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 1-201362426-T-G is Benign according to our data. Variant chr1-201362426-T-G is described in ClinVar as [Benign]. Clinvar id is 256845.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-201362426-T-G is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNNT2 | NM_001276345.2 | c.601-32A>C | intron_variant | ENST00000656932.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNNT2 | ENST00000656932.1 | c.601-32A>C | intron_variant | NM_001276345.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.741 AC: 112517AN: 151940Hom.: 41769 Cov.: 32
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GnomAD3 exomes AF: 0.735 AC: 180715AN: 245982Hom.: 66911 AF XY: 0.739 AC XY: 98251AN XY: 133028
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GnomAD4 exome AF: 0.721 AC: 1051935AN: 1459238Hom.: 380759 Cov.: 40 AF XY: 0.725 AC XY: 525962AN XY: 725692
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GnomAD4 genome ? AF: 0.741 AC: 112611AN: 152058Hom.: 41807 Cov.: 32 AF XY: 0.745 AC XY: 55411AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hypertrophic cardiomyopathy 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Dilated cardiomyopathy 1D Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Cardiomyopathy, familial restrictive, 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
La Branchor
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at