7-128848980-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_001458.5(FLNC):c.4925C>T(p.Thr1642Ile) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/23 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1642R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001458.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.4925C>T | p.Thr1642Ile | missense_variant, splice_region_variant | 28/48 | ENST00000325888.13 | |
FLNC | NM_001127487.2 | c.4925C>T | p.Thr1642Ile | missense_variant, splice_region_variant | 28/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.4925C>T | p.Thr1642Ile | missense_variant, splice_region_variant | 28/48 | 1 | NM_001458.5 | P3 | |
FLNC | ENST00000346177.6 | c.4925C>T | p.Thr1642Ile | missense_variant, splice_region_variant | 28/47 | 1 | A1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000411 AC: 1AN: 243272Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132428
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1458860Hom.: 0 Cov.: 35 AF XY: 0.00000276 AC XY: 2AN XY: 725388
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 22, 2018 | This sequence change replaces threonine with isoleucine at codon 1642 of the FLNC protein (p.Thr1642Ile). The threonine residue is highly conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is present in population databases (rs756074974, ExAC 0.002%). This variant has not been reported in the literature in individuals with FLNC-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at