rs782555930
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_001110556.2(FLNA):c.7568G>A(p.Ser2523Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,211,457 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 48 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.7568G>A | p.Ser2523Asn | missense_variant | Exon 47 of 48 | ENST00000369850.10 | NP_001104026.1 | |
FLNA | NM_001456.4 | c.7544G>A | p.Ser2515Asn | missense_variant | Exon 46 of 47 | NP_001447.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000167 AC: 19AN: 113525Hom.: 0 Cov.: 26 AF XY: 0.000224 AC XY: 8AN XY: 35647
GnomAD3 exomes AF: 0.000392 AC: 71AN: 181325Hom.: 0 AF XY: 0.000341 AC XY: 23AN XY: 67521
GnomAD4 exome AF: 0.000115 AC: 126AN: 1097877Hom.: 0 Cov.: 33 AF XY: 0.000110 AC XY: 40AN XY: 363337
GnomAD4 genome AF: 0.000167 AC: 19AN: 113580Hom.: 0 Cov.: 26 AF XY: 0.000224 AC XY: 8AN XY: 35712
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
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
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at