rs781798819
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_001110556.2(FLNA):āc.2027A>Gā(p.Lys676Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000505 in 1,207,247 control chromosomes in the GnomAD database, including 1 homozygotes. There are 21 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K676N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.2027A>G | p.Lys676Arg | missense_variant | 14/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.2027A>G | p.Lys676Arg | missense_variant | 14/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.2027A>G | p.Lys676Arg | missense_variant | 14/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.000135 AC: 15AN: 111055Hom.: 0 Cov.: 22 AF XY: 0.000150 AC XY: 5AN XY: 33279
GnomAD3 exomes AF: 0.000154 AC: 28AN: 181407Hom.: 1 AF XY: 0.000163 AC XY: 11AN XY: 67543
GnomAD4 exome AF: 0.0000420 AC: 46AN: 1096137Hom.: 1 Cov.: 32 AF XY: 0.0000442 AC XY: 16AN XY: 361845
GnomAD4 genome ? AF: 0.000135 AC: 15AN: 111110Hom.: 0 Cov.: 22 AF XY: 0.000150 AC XY: 5AN XY: 33344
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 28, 2017 | 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. - |
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 14, 2022 | 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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
FLNA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 20, 2022 | This variant is classified as likely 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