rs572952653
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4BP6BS1BS2
The NM_001458.5(FLNC):c.7291G>A(p.Val2431Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000397 in 1,612,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2431L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001458.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.7291G>A | p.Val2431Met | missense_variant | 44/48 | ENST00000325888.13 | |
FLNC-AS1 | NR_149055.1 | n.103-3160C>T | intron_variant, non_coding_transcript_variant | ||||
FLNC | NM_001127487.2 | c.7192G>A | p.Val2398Met | missense_variant | 43/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.7291G>A | p.Val2431Met | missense_variant | 44/48 | 1 | NM_001458.5 | P3 | |
FLNC | ENST00000346177.6 | c.7192G>A | p.Val2398Met | missense_variant | 43/47 | 1 | A1 | ||
FLNC-AS1 | ENST00000469965.1 | n.103-3160C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000190 AC: 47AN: 246748Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 134198
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1460608Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23AN XY: 726726
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74482
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 30, 2016 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at