rs7063300
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001110556.2(FLNA):c.7756+11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.69 ( 19867 hom., 24581 hem., cov: 26)
Exomes 𝑓: 0.58 ( 129760 hom. 213779 hem. )
Failed GnomAD Quality Control
Consequence
FLNA
NM_001110556.2 intron
NM_001110556.2 intron
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.12
Genes affected
FLNA (HGNC:3754): (filamin A) The protein encoded by this gene is an actin-binding protein that crosslinks actin filaments and links actin filaments to membrane glycoproteins. The encoded protein is involved in remodeling the cytoskeleton to effect changes in cell shape and migration. This protein interacts with integrins, transmembrane receptor complexes, and second messengers. Defects in this gene are a cause of several syndromes, including periventricular nodular heterotopias (PVNH1, PVNH4), otopalatodigital syndromes (OPD1, OPD2), frontometaphyseal dysplasia (FMD), Melnick-Needles syndrome (MNS), and X-linked congenital idiopathic intestinal pseudoobstruction (CIIPX). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.7756+11T>C | intron_variant | ENST00000369850.10 | |||
FLNA | NM_001456.4 | c.7732+11T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.7756+11T>C | intron_variant | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes AF: 0.693 AC: 77982AN: 112593Hom.: 19860 Cov.: 26 AF XY: 0.706 AC XY: 24523AN XY: 34757
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.584 AC: 638757AN: 1092843Hom.: 129760 Cov.: 34 AF XY: 0.595 AC XY: 213779AN XY: 359097
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.693 AC: 78045AN: 112643Hom.: 19867 Cov.: 26 AF XY: 0.706 AC XY: 24581AN XY: 34817
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ClinVar
Not reported inComputational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at