rs782239678
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001110556.2(FLNA):c.2839G>A(p.Val947Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000045 in 1,200,657 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 31 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.2839G>A | p.Val947Ile | missense_variant | Exon 20 of 48 | ENST00000369850.10 | NP_001104026.1 | |
FLNA | NM_001456.4 | c.2839G>A | p.Val947Ile | missense_variant | Exon 20 of 47 | NP_001447.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000362 AC: 4AN: 110605Hom.: 0 Cov.: 23 AF XY: 0.0000305 AC XY: 1AN XY: 32815
GnomAD3 exomes AF: 0.0000882 AC: 16AN: 181324Hom.: 0 AF XY: 0.000134 AC XY: 9AN XY: 67412
GnomAD4 exome AF: 0.0000459 AC: 50AN: 1089997Hom.: 0 Cov.: 31 AF XY: 0.0000843 AC XY: 30AN XY: 355709
GnomAD4 genome AF: 0.0000361 AC: 4AN: 110660Hom.: 0 Cov.: 23 AF XY: 0.0000304 AC XY: 1AN XY: 32880
ClinVar
Submissions by phenotype
not specified Benign:1
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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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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at