rs201603843
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_001110556.2(FLNA):c.2516C>T(p.Thr839Met) variant causes a missense change. The variant allele was found at a frequency of 0.000172 in 1,210,576 control chromosomes in the GnomAD database, including 1 homozygotes. There are 75 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T839A) has been classified as Benign.
Frequency
Consequence
NM_001110556.2 missense
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.2516C>T | p.Thr839Met | missense_variant | 17/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.2516C>T | p.Thr839Met | missense_variant | 17/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.2516C>T | p.Thr839Met | missense_variant | 17/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.000203 AC: 23AN: 113151Hom.: 0 Cov.: 23 AF XY: 0.000283 AC XY: 10AN XY: 35283
GnomAD3 exomes AF: 0.000331 AC: 60AN: 181269Hom.: 1 AF XY: 0.000311 AC XY: 21AN XY: 67531
GnomAD4 exome AF: 0.000169 AC: 185AN: 1097425Hom.: 1 Cov.: 33 AF XY: 0.000179 AC XY: 65AN XY: 363033
GnomAD4 genome ? AF: 0.000203 AC: 23AN: 113151Hom.: 0 Cov.: 23 AF XY: 0.000283 AC XY: 10AN XY: 35283
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2017 | This alteration is classified as 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Melnick-Needles syndrome;C0262436:Cardiac valvular dysplasia, X-linked;C0265251:Oto-palato-digital syndrome, type I;C1844696:Oto-palato-digital syndrome, type II;C1845902:FG syndrome 2;C1846129:Terminal osseous dysplasia-pigmentary defects syndrome;C1848213:Heterotopia, periventricular, X-linked dominant;C2746068:Intestinal pseudoobstruction, neuronal, chronic idiopathic, X-linked;C4281559:Frontometaphyseal dysplasia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 09, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 13, 2020 | Has not been previously published as pathogenic or benign to our knowledge - |
FLNA-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 10, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at