chrX-154348863-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 5P and 2B. PM2PM5PP2BP4_Moderate
The NM_001110556.2(FLNA):c.7930G>A(p.Val2644Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 Uncertain significance (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V2644L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.7930G>A | p.Val2644Ile | missense_variant | 48/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.7906G>A | p.Val2636Ile | missense_variant | 47/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.7930G>A | p.Val2644Ile | missense_variant | 48/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 exomes AF: 0.00000569 AC: 1AN: 175847Hom.: 0 AF XY: 0.0000157 AC XY: 1AN XY: 63571
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000366 AC: 4AN: 1093757Hom.: 0 Cov.: 30 AF XY: 0.00000278 AC XY: 1AN XY: 360089
GnomAD4 genome ? Cov.: 24
ClinVar
Submissions by phenotype
Developmental delay Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at