1-74489216-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015978.3(TNNI3K):āc.2149A>Gā(p.Met717Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000194 in 1,612,340 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_015978.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNNI3K | NM_015978.3 | c.2149A>G | p.Met717Val | missense_variant | 22/25 | ENST00000326637.8 | NP_057062.1 | |
FPGT-TNNI3K | NM_001112808.3 | c.2452A>G | p.Met818Val | missense_variant | 24/27 | NP_001106279.3 | ||
LRRC53 | NM_001382280.1 | c.-26-5841T>C | intron_variant | ENST00000294635.5 | NP_001369209.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNNI3K | ENST00000326637.8 | c.2149A>G | p.Met717Val | missense_variant | 22/25 | 1 | NM_015978.3 | ENSP00000322251 | P1 | |
LRRC53 | ENST00000294635.5 | c.-26-5841T>C | intron_variant | 5 | NM_001382280.1 | ENSP00000294635 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000393 AC: 98AN: 249602Hom.: 0 AF XY: 0.000304 AC XY: 41AN XY: 134956
GnomAD4 exome AF: 0.000179 AC: 262AN: 1460000Hom.: 0 Cov.: 30 AF XY: 0.000169 AC XY: 123AN XY: 726338
GnomAD4 genome AF: 0.000335 AC: 51AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
TNNI3K-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 01, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at