rs11210449

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17
Variant links:
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]

Genome browser will be placed here

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 Protein UniProt
TNNI3KNM_015978.3 linkuse as main transcriptc.445-11143A>G intron_variant ENST00000326637.8 NP_057062.1
FPGT-TNNI3KNM_001112808.3 linkuse as main transcriptc.748-11143A>G intron_variant NP_001106279.3
FPGT-TNNI3KNM_001199327.2 linkuse as main transcriptc.748-11143A>G intron_variant NP_001186256.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNNI3KENST00000326637.8 linkuse as main transcriptc.445-11143A>G intron_variant 1 NM_015978.3 ENSP00000322251 P1Q59H18-2

Frequencies

GnomAD3 genomes
AF:
0.595
AC:
90371
AN:
151882
Hom.:
30415
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.246
Gnomad AMI
AF:
0.633
Gnomad AMR
AF:
0.686
Gnomad ASJ
AF:
0.746
Gnomad EAS
AF:
0.819
Gnomad SAS
AF:
0.696
Gnomad FIN
AF:
0.716
Gnomad MID
AF:
0.731
Gnomad NFE
AF:
0.733
Gnomad OTH
AF:
0.659
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.595
AC:
90381
AN:
152000
Hom.:
30416
Cov.:
32
AF XY:
0.598
AC XY:
44437
AN XY:
74286
show subpopulations
Gnomad4 AFR
AF:
0.246
Gnomad4 AMR
AF:
0.686
Gnomad4 ASJ
AF:
0.746
Gnomad4 EAS
AF:
0.819
Gnomad4 SAS
AF:
0.697
Gnomad4 FIN
AF:
0.716
Gnomad4 NFE
AF:
0.733
Gnomad4 OTH
AF:
0.656
Alfa
AF:
0.628
Hom.:
4287
Bravo
AF:
0.578
Asia WGS
AF:
0.683
AC:
2378
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
12
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11210449; hg19: chr1-74785991; API