rs79790270
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001458.5(FLNC):c.5669-12C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 1,613,920 control chromosomes in the GnomAD database, including 1,150 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.028 ( 93 hom., cov: 33)
Exomes 𝑓: 0.034 ( 1057 hom. )
Consequence
FLNC
NM_001458.5 splice_polypyrimidine_tract, intron
NM_001458.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0003501
2
Clinical Significance
Conservation
PhyloP100: -0.0410
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 made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BP6
?
Variant 7-128851443-C-T is Benign according to our data. Variant chr7-128851443-C-T is described in ClinVar as [Benign]. Clinvar id is 258149.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-128851443-C-T is described in Lovd as [Benign]. Variant chr7-128851443-C-T is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0275 (4189/152324) while in subpopulation NFE AF= 0.0377 (2567/68028). AF 95% confidence interval is 0.0365. There are 93 homozygotes in gnomad4. There are 2170 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 4189 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNC | NM_001458.5 | c.5669-12C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000325888.13 | |||
FLNC-AS1 | NR_149055.1 | n.273G>A | non_coding_transcript_exon_variant | 3/4 | |||
FLNC | NM_001127487.2 | c.5570-12C>T | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNC | ENST00000325888.13 | c.5669-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001458.5 | P3 | |||
FLNC | ENST00000346177.6 | c.5570-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | A1 | ||||
FLNC-AS1 | ENST00000469965.1 | n.273G>A | non_coding_transcript_exon_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0275 AC: 4190AN: 152206Hom.: 93 Cov.: 33
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GnomAD3 exomes AF: 0.0312 AC: 7794AN: 249420Hom.: 208 AF XY: 0.0318 AC XY: 4309AN XY: 135356
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GnomAD4 exome AF: 0.0343 AC: 50078AN: 1461596Hom.: 1057 Cov.: 34 AF XY: 0.0346 AC XY: 25148AN XY: 727108
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GnomAD4 genome ? AF: 0.0275 AC: 4189AN: 152324Hom.: 93 Cov.: 33 AF XY: 0.0291 AC XY: 2170AN XY: 74482
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ClinVar
Significance: Benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:7
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 29, 2023 | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | 5669-12C>T in intron 34 of FLNC: This variant is not expected to have clinical s ignificance because it has been identified in 3.5% (300/8532) of European Americ an chromosomes from a broad population by the NHLBI Exome Sequencing Project (ht tp://evs.gs.washington.edu/EVS; dbSNP rs79790270). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 13, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Myofibrillar myopathy 5;C3279722:Distal myopathy with posterior leg and anterior hand involvement;C4310749:Hypertrophic cardiomyopathy 26;CN239310:Dilated Cardiomyopathy, Dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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