rs774600814
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001458.5(FLNC):c.5427G>A(p.Thr1809=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000706 in 1,613,646 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. T1809T) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.5427G>A | p.Thr1809= | synonymous_variant | 33/48 | ENST00000325888.13 | |
FLNC-AS1 | NR_149055.1 | n.316-426C>T | intron_variant, non_coding_transcript_variant | ||||
FLNC | NM_001127487.2 | c.5328G>A | p.Thr1776= | synonymous_variant | 32/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.5427G>A | p.Thr1809= | synonymous_variant | 33/48 | 1 | NM_001458.5 | P3 | |
FLNC | ENST00000346177.6 | c.5328G>A | p.Thr1776= | synonymous_variant | 32/47 | 1 | A1 | ||
FLNC-AS1 | ENST00000469965.1 | n.316-426C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152050Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249388Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135336
GnomAD4 exome AF: 0.0000691 AC: 101AN: 1461596Hom.: 0 Cov.: 34 AF XY: 0.0000578 AC XY: 42AN XY: 727116
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152050Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74270
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | FLNC: BP4, BP7 - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2019 | 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 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at