rs10920185
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001276345.2(TNNT2):c.41+75C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,446,756 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0090 ( 16 hom., cov: 33)
Exomes 𝑓: 0.00089 ( 17 hom. )
Consequence
TNNT2
NM_001276345.2 intron
NM_001276345.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.85
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 1-201373139-G-C is Benign according to our data. Variant chr1-201373139-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1223114.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00896 (1365/152284) while in subpopulation AFR AF= 0.0319 (1325/41546). AF 95% confidence interval is 0.0305. There are 16 homozygotes in gnomad4. There are 662 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1365 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNNT2 | NM_001276345.2 | c.41+75C>G | intron_variant | ENST00000656932.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNNT2 | ENST00000656932.1 | c.41+75C>G | intron_variant | NM_001276345.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00897 AC: 1365AN: 152166Hom.: 16 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00236 AC: 593AN: 251160Hom.: 11 AF XY: 0.00182 AC XY: 247AN XY: 135796
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GnomAD4 exome AF: 0.000892 AC: 1155AN: 1294472Hom.: 17 Cov.: 19 AF XY: 0.000761 AC XY: 497AN XY: 653450
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GnomAD4 genome ? AF: 0.00896 AC: 1365AN: 152284Hom.: 16 Cov.: 33 AF XY: 0.00889 AC XY: 662AN XY: 74466
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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 | Jul 05, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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