1-74235611-T-A
Position:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_015978.3(TNNI3K):c.40+120T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.993 in 543,176 control chromosomes in the GnomAD database, including 267,765 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.98 ( 72831 hom., cov: 31)
Exomes 𝑓: 1.0 ( 194934 hom. )
Consequence
TNNI3K
NM_015978.3 intron
NM_015978.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.02
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 1-74235611-T-A is Benign according to our data. Variant chr1-74235611-T-A is described in ClinVar as [Benign]. Clinvar id is 1273965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNNI3K | NM_015978.3 | c.40+120T>A | intron_variant | ENST00000326637.8 | |||
FPGT-TNNI3K | NM_001112808.3 | c.344-491T>A | intron_variant | ||||
FPGT-TNNI3K | NM_001199327.2 | c.344-491T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNNI3K | ENST00000326637.8 | c.40+120T>A | intron_variant | 1 | NM_015978.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.979 AC: 148419AN: 151528Hom.: 72770 Cov.: 31
GnomAD3 genomes
AF:
AC:
148419
AN:
151528
Hom.:
Cov.:
31
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: 0.998 AC: 390676AN: 391530Hom.: 194934 AF XY: 0.998 AC XY: 206489AN XY: 206858
GnomAD4 exome
AF:
AC:
390676
AN:
391530
Hom.:
AF XY:
AC XY:
206489
AN XY:
206858
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: 0.980 AC: 148539AN: 151646Hom.: 72831 Cov.: 31 AF XY: 0.980 AC XY: 72641AN XY: 74122
GnomAD4 genome
AF:
AC:
148539
AN:
151646
Hom.:
Cov.:
31
AF XY:
AC XY:
72641
AN XY:
74122
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:
Asia WGS
AF:
AC:
3455
AN:
3468
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 04, 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