1-74235967-A-T
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015978.3(TNNI3K):c.41-135A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 547,348 control chromosomes in the GnomAD database, including 52,863 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.38 ( 12014 hom., cov: 32)
Exomes 𝑓: 0.44 ( 40849 hom. )
Consequence
TNNI3K
NM_015978.3 intron
NM_015978.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.333
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 1-74235967-A-T is Benign according to our data. Variant chr1-74235967-A-T is described in ClinVar as [Benign]. Clinvar id is 1258735.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNNI3K | NM_015978.3 | c.41-135A>T | intron_variant | ENST00000326637.8 | NP_057062.1 | |||
FPGT-TNNI3K | NM_001112808.3 | c.344-135A>T | intron_variant | NP_001106279.3 | ||||
FPGT-TNNI3K | NM_001199327.2 | c.344-135A>T | intron_variant | NP_001186256.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNNI3K | ENST00000326637.8 | c.41-135A>T | intron_variant | 1 | NM_015978.3 | ENSP00000322251 | P1 |
Frequencies
GnomAD3 genomes AF: 0.379 AC: 57252AN: 151232Hom.: 12022 Cov.: 32
GnomAD3 genomes
AF:
AC:
57252
AN:
151232
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.445 AC: 176168AN: 396000Hom.: 40849 AF XY: 0.448 AC XY: 92413AN XY: 206152
GnomAD4 exome
AF:
AC:
176168
AN:
396000
Hom.:
AF XY:
AC XY:
92413
AN XY:
206152
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.378 AC: 57252AN: 151348Hom.: 12014 Cov.: 32 AF XY: 0.385 AC XY: 28493AN XY: 73956
GnomAD4 genome
AF:
AC:
57252
AN:
151348
Hom.:
Cov.:
32
AF XY:
AC XY:
28493
AN XY:
73956
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 01, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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