X-154358217-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001110556.2(FLNA):c.4737G>A(p.Leu1579=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,209,509 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L1579L) has been classified as Likely benign.
Frequency
Consequence
NM_001110556.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.4737G>A | p.Leu1579= | synonymous_variant | 28/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.4737G>A | p.Leu1579= | synonymous_variant | 28/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.4737G>A | p.Leu1579= | synonymous_variant | 28/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000355 AC: 4AN: 112666Hom.: 0 Cov.: 24 AF XY: 0.0000575 AC XY: 2AN XY: 34794
GnomAD3 exomes AF: 0.00000562 AC: 1AN: 178008Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65684
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1096843Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 362901
GnomAD4 genome ? AF: 0.0000355 AC: 4AN: 112666Hom.: 0 Cov.: 24 AF XY: 0.0000575 AC XY: 2AN XY: 34794
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 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. - |
Melnick-Needles syndrome;C0265293:Frontometaphyseal dysplasia;C1844696:Oto-palato-digital syndrome, type II;C1848213:Heterotopia, periventricular, X-linked dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at