rs1514177

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015978.3(TNNI3K):​c.2352-14516C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,968 control chromosomes in the GnomAD database, including 18,896 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 0.49 ( 18896 hom., cov: 32)

Consequence

TNNI3K
NM_015978.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0590
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=-0.79).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TNNI3KNM_015978.3 linkuse as main transcriptc.2352-14516C>G intron_variant ENST00000326637.8 NP_057062.1
FPGT-TNNI3KNM_001112808.3 linkuse as main transcriptc.2655-14516C>G intron_variant NP_001106279.3
LRRC53XM_011542512.4 linkuse as main transcriptc.49+11086G>C intron_variant XP_011540814.2
LRRC53XM_017003081.2 linkuse as main transcriptc.49+11086G>C intron_variant XP_016858570.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNNI3KENST00000326637.8 linkuse as main transcriptc.2352-14516C>G intron_variant 1 NM_015978.3 ENSP00000322251 P1Q59H18-2

Frequencies

GnomAD3 genomes
AF:
0.489
AC:
74180
AN:
151850
Hom.:
18887
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.371
Gnomad AMI
AF:
0.628
Gnomad AMR
AF:
0.456
Gnomad ASJ
AF:
0.617
Gnomad EAS
AF:
0.242
Gnomad SAS
AF:
0.467
Gnomad FIN
AF:
0.518
Gnomad MID
AF:
0.566
Gnomad NFE
AF:
0.573
Gnomad OTH
AF:
0.525
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.488
AC:
74205
AN:
151968
Hom.:
18896
Cov.:
32
AF XY:
0.482
AC XY:
35779
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.370
Gnomad4 AMR
AF:
0.455
Gnomad4 ASJ
AF:
0.617
Gnomad4 EAS
AF:
0.243
Gnomad4 SAS
AF:
0.466
Gnomad4 FIN
AF:
0.518
Gnomad4 NFE
AF:
0.573
Gnomad4 OTH
AF:
0.524
Alfa
AF:
0.535
Hom.:
2770
Bravo
AF:
0.475
Asia WGS
AF:
0.400
AC:
1395
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
6.7
DANN
Benign
0.78

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: rs1514177; hg19: chr1-74991402; API