rs782546714
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP6BS2
The NM_001110556.2(FLNA):c.3094C>T(p.Arg1032Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000298 in 1,208,646 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1032H) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.3094C>T | p.Arg1032Cys | missense_variant | 21/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.3094C>T | p.Arg1032Cys | missense_variant | 21/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.3094C>T | p.Arg1032Cys | missense_variant | 21/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000630 AC: 7AN: 111029Hom.: 0 Cov.: 22 AF XY: 0.0000602 AC XY: 2AN XY: 33241
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181371Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67499
GnomAD4 exome AF: 0.0000264 AC: 29AN: 1097617Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 11AN XY: 363279
GnomAD4 genome ? AF: 0.0000630 AC: 7AN: 111029Hom.: 0 Cov.: 22 AF XY: 0.0000602 AC XY: 2AN XY: 33241
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 08, 2019 | Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar (ClinVar Variant ID# 547382; Landrum et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 30986657) - |
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 16, 2024 | - - |
Connective tissue disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Human Genetics, Inc, Center for Human Genetics, Inc | Nov 01, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at