rs1444704657
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001458.5(FLNC):c.7781-3C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FLNC
NM_001458.5 splice_region, intron
NM_001458.5 splice_region, intron
Scores
2
Splicing: ADA: 0.02016
2
Clinical Significance
Conservation
PhyloP100: 2.41
Publications
0 publications found
Genes affected
FLNC (HGNC:3756): (filamin C) This gene encodes one of three related filamin genes, specifically gamma filamin. These filamin proteins crosslink actin filaments into orthogonal networks in cortical cytoplasm and participate in the anchoring of membrane proteins for the actin cytoskeleton. Three functional domains exist in filamin: an N-terminal filamentous actin-binding domain, a C-terminal self-association domain, and a membrane glycoprotein-binding domain. Mutations in this gene are a cause of cardiopathy. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001458.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FLNC | NM_001458.5 | MANE Select | c.7781-3C>T | splice_region intron | N/A | NP_001449.3 | |||
| FLNC | NM_001127487.2 | c.7682-3C>T | splice_region intron | N/A | NP_001120959.1 | ||||
| FLNC-AS1 | NR_149055.1 | n.102+4520G>A | intron | N/A |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FLNC | ENST00000325888.13 | TSL:1 MANE Select | c.7781-3C>T | splice_region intron | N/A | ENSP00000327145.8 | |||
| FLNC | ENST00000346177.6 | TSL:1 | c.7682-3C>T | splice_region intron | N/A | ENSP00000344002.6 | |||
| FLNC | ENST00000714183.1 | c.7643-3C>T | splice_region intron | N/A | ENSP00000519472.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 179318 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
179318
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1366866Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 681284
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1366866
Hom.:
Cov.:
22
AF XY:
AC XY:
0
AN XY:
681284
African (AFR)
AF:
AC:
0
AN:
31778
American (AMR)
AF:
AC:
0
AN:
40260
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25140
East Asian (EAS)
AF:
AC:
0
AN:
37762
South Asian (SAS)
AF:
AC:
0
AN:
80388
European-Finnish (FIN)
AF:
AC:
0
AN:
50802
Middle Eastern (MID)
AF:
AC:
0
AN:
5354
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1038336
Other (OTH)
AF:
AC:
0
AN:
57046
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions as Germline
Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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