7-128842691-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001458.5(FLNC):c.2382G>A(p.Ala794=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000983 in 1,556,234 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A794A) has been classified as Likely benign.
Frequency
Consequence
NM_001458.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.2382G>A | p.Ala794= | synonymous_variant | 15/48 | ENST00000325888.13 | |
FLNC | NM_001127487.2 | c.2382G>A | p.Ala794= | synonymous_variant | 15/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.2382G>A | p.Ala794= | synonymous_variant | 15/48 | 1 | NM_001458.5 | P3 | |
FLNC | ENST00000346177.6 | c.2382G>A | p.Ala794= | synonymous_variant | 15/47 | 1 | A1 | ||
FLNC | ENST00000388853.3 | n.498G>A | non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000366 AC: 58AN: 158620Hom.: 0 AF XY: 0.000331 AC XY: 28AN XY: 84634
GnomAD4 exome AF: 0.0000983 AC: 138AN: 1403938Hom.: 0 Cov.: 47 AF XY: 0.000102 AC XY: 71AN XY: 692886
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 29, 2018 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 21, 2020 | 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 24, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at