chrX-154362500-C-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP6_Moderate
The NM_001110556.2(FLNA):āc.2483G>Cā(p.Arg828Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000638 in 1,097,197 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R828H) has been classified as Uncertain significance.
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 | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.2483G>C | p.Arg828Pro | missense_variant | 17/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.2483G>C | p.Arg828Pro | missense_variant | 17/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.2483G>C | p.Arg828Pro | missense_variant | 17/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.00000552 AC: 1AN: 181129Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67429
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1097197Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 1AN XY: 362905
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Melnick-Needles syndrome;C0265293:Frontometaphyseal dysplasia;C1844696:Oto-palato-digital syndrome, type II;C1848213:Heterotopia, periventricular, X-linked dominant Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at