X-154354983-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4BP6
The NM_001110556.2(FLNA):āc.5059A>Gā(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).
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.5059A>G | p.Thr1687Ala | missense_variant | 31/48 | ENST00000369850.10 | NP_001104026.1 | |
FLNA | NM_001456.4 | c.5035A>G | p.Thr1679Ala | missense_variant | 30/47 | NP_001447.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.5059A>G | p.Thr1687Ala | missense_variant | 31/48 | 1 | NM_001110556.2 | ENSP00000358866 |
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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at