rs782469665
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4BP6BS2
The NM_001110556.2(FLNA):c.5059A>G(p.Thr1687Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000578 in 1,211,243 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. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T1687T) has been classified as Likely benign.
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.5059A>G | p.Thr1687Ala | missense_variant | 31/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.5035A>G | p.Thr1679Ala | missense_variant | 30/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.5059A>G | p.Thr1687Ala | missense_variant | 31/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000176 AC: 2AN: 113424Hom.: 0 Cov.: 26 AF XY: 0.0000281 AC XY: 1AN XY: 35560
GnomAD3 exomes AF: 0.0000220 AC: 4AN: 181461Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67561
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1097819Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 1AN XY: 363365
GnomAD4 genome ? AF: 0.0000176 AC: 2AN: 113424Hom.: 0 Cov.: 26 AF XY: 0.0000281 AC XY: 1AN XY: 35560
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Dec 28, 2022 | The FLNA c.5035A>G; p.Thr1679Ala variant (rs782469665), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 569597). This variant is found in the general population with an overall allele frequency of 0.002% (4/181461 alleles, including 2 hemizygotes) in the Genome Aggregation Database. Computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.272). Due to limited information, the clinical significance of this variant is uncertain at this time. - |
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 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at