chr1-74235478-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_015978.3(TNNI3K):c.27C>A(p.Thr9Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TNNI3K
NM_015978.3 synonymous
NM_015978.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.35
Publications
0 publications found
Genes affected
TNNI3K (HGNC:19661): (TNNI3 interacting kinase) This gene encodes a protein that belongs to the MAP kinase kinase kinase (MAPKKK) family of protein kinases. The protein contains ankyrin repeat, protein kinase and serine-rich domains and is thought to play a role in cardiac physiology. [provided by RefSeq, Sep 2012]
FPGT-TNNI3K (HGNC:42952): (FPGT-TNNI3K readthrough) Enables protein C-terminus binding activity; protein kinase activity; and troponin I binding activity. Involved in protein phosphorylation and regulation of heart contraction. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
Variant 1-74235478-C-A is Benign according to our data. Variant chr1-74235478-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2705577.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-1.35 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| TNNI3K | NM_015978.3 | c.27C>A | p.Thr9Thr | synonymous_variant | Exon 1 of 25 | ENST00000326637.8 | NP_057062.1 | |
| FPGT-TNNI3K | NM_001112808.3 | c.344-624C>A | intron_variant | Intron 3 of 26 | NP_001106279.3 | |||
| FPGT-TNNI3K | NM_001199327.2 | c.344-624C>A | intron_variant | Intron 3 of 23 | NP_001186256.3 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1346068Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 674650
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1346068
Hom.:
Cov.:
23
AF XY:
AC XY:
0
AN XY:
674650
African (AFR)
AF:
AC:
0
AN:
29444
American (AMR)
AF:
AC:
0
AN:
36536
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24864
East Asian (EAS)
AF:
AC:
0
AN:
37608
South Asian (SAS)
AF:
AC:
0
AN:
79148
European-Finnish (FIN)
AF:
AC:
0
AN:
53080
Middle Eastern (MID)
AF:
AC:
0
AN:
5512
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1023686
Other (OTH)
AF:
AC:
0
AN:
56190
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Dec 26, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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