X-154360540-G-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001110556.2(FLNA):c.3255C>A(p.Pro1085=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,208,566 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. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P1085P) has been classified as Likely benign.
Frequency
Consequence
NM_001110556.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.3255C>A | p.Pro1085= | synonymous_variant | 22/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.3255C>A | p.Pro1085= | synonymous_variant | 22/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.3255C>A | p.Pro1085= | synonymous_variant | 22/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000177 AC: 2AN: 113234Hom.: 0 Cov.: 25 AF XY: 0.0000283 AC XY: 1AN XY: 35372
GnomAD3 exomes AF: 0.00000573 AC: 1AN: 174530Hom.: 0 AF XY: 0.0000156 AC XY: 1AN XY: 64112
GnomAD4 exome AF: 0.00000274 AC: 3AN: 1095332Hom.: 0 Cov.: 33 AF XY: 0.00000276 AC XY: 1AN XY: 361866
GnomAD4 genome ? AF: 0.0000177 AC: 2AN: 113234Hom.: 0 Cov.: 25 AF XY: 0.0000283 AC XY: 1AN XY: 35372
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 | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at