rs782390251
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_001110556.2(FLNA):c.5451G>A(p.Gln1817=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000578 in 1,210,842 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000088 ( 0 hom., 0 hem., cov: 26)
Exomes 𝑓: 0.0000055 ( 0 hom. 2 hem. )
Consequence
FLNA
NM_001110556.2 synonymous
NM_001110556.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.228
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 Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP7
Synonymous conserved (PhyloP=0.228 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.5451G>A | p.Gln1817= | synonymous_variant | 34/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.5427G>A | p.Gln1809= | synonymous_variant | 33/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.5451G>A | p.Gln1817= | synonymous_variant | 34/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes AF: 0.00000882 AC: 1AN: 113390Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35530
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GnomAD3 exomes AF: 0.0000221 AC: 4AN: 180796Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67210
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GnomAD4 exome AF: 0.00000547 AC: 6AN: 1097399Hom.: 0 Cov.: 33 AF XY: 0.00000551 AC XY: 2AN XY: 363189
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GnomAD4 genome AF: 0.00000881 AC: 1AN: 113443Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35593
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 15, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at