rs782351877
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PP2PP3_ModerateBP6BS2
The NM_001110556.2(FLNA):c.5098G>A(p.Val1700Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 1,211,348 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic 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. V1700V) 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.5098G>A | p.Val1700Met | missense_variant | 31/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.5074G>A | p.Val1692Met | missense_variant | 30/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.5098G>A | p.Val1700Met | missense_variant | 31/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000881 AC: 1AN: 113506Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35632
GnomAD3 exomes AF: 0.0000330 AC: 6AN: 181596Hom.: 0 AF XY: 0.0000296 AC XY: 2AN XY: 67614
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1097842Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363410
GnomAD4 genome ? AF: 0.00000881 AC: 1AN: 113506Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 35632
ClinVar
Submissions by phenotype
Intellectual disability Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Diagnostic Laboratory, Strasbourg University Hospital | Sep 10, 2020 | - - |
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 | Jul 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at