rs11210449
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015978.3(TNNI3K):c.445-11143A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,000 control chromosomes in the GnomAD database, including 30,416 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.59 ( 30416 hom., cov: 32)
Consequence
TNNI3K
NM_015978.3 intron
NM_015978.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.17
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNNI3K | NM_015978.3 | c.445-11143A>G | intron_variant | ENST00000326637.8 | |||
FPGT-TNNI3K | NM_001112808.3 | c.748-11143A>G | intron_variant | ||||
FPGT-TNNI3K | NM_001199327.2 | c.748-11143A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNNI3K | ENST00000326637.8 | c.445-11143A>G | intron_variant | 1 | NM_015978.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.595 AC: 90371AN: 151882Hom.: 30415 Cov.: 32
GnomAD3 genomes
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90371
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.595 AC: 90381AN: 152000Hom.: 30416 Cov.: 32 AF XY: 0.598 AC XY: 44437AN XY: 74286
GnomAD4 genome
?
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90381
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152000
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32
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44437
AN XY:
74286
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Asia WGS
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2378
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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