rs781993962
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 2P and 18B. PP2PP3BP4_ModerateBP6_Very_StrongBS1BS2
The NM_001110556.2(FLNA):c.7822C>T(p.His2608Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000076 in 1,209,883 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 53 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. H2608H) has been classified as Likely benign.
Frequency
Consequence
NM_001110556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.7822C>T | p.His2608Tyr | missense_variant | 48/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.7798C>T | p.His2600Tyr | missense_variant | 47/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.7822C>T | p.His2608Tyr | missense_variant | 48/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000267 AC: 3AN: 112267Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34429
GnomAD3 exomes AF: 0.000182 AC: 33AN: 180822Hom.: 0 AF XY: 0.000357 AC XY: 24AN XY: 67190
GnomAD4 exome AF: 0.0000811 AC: 89AN: 1097563Hom.: 0 Cov.: 31 AF XY: 0.000146 AC XY: 53AN XY: 363139
GnomAD4 genome ? AF: 0.0000267 AC: 3AN: 112320Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 34492
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
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 05, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2020 | Reported in an individual with single suture craniosynostosis (Clarke et al., 2018); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 29168297) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at