rs782765195
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_001110556.2(FLNA):āc.1542G>Cā(p.Glu514Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 1,210,760 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.1542G>C | p.Glu514Asp | missense_variant | 10/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.1542G>C | p.Glu514Asp | missense_variant | 10/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.1542G>C | p.Glu514Asp | missense_variant | 10/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000266 AC: 3AN: 112927Hom.: 0 Cov.: 24 AF XY: 0.0000285 AC XY: 1AN XY: 35073
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 181477Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67609
GnomAD4 exome AF: 0.0000118 AC: 13AN: 1097833Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 2AN XY: 363389
GnomAD4 genome ? AF: 0.0000266 AC: 3AN: 112927Hom.: 0 Cov.: 24 AF XY: 0.0000285 AC XY: 1AN XY: 35073
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 24, 2018 | - - |
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 | Mar 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at