chrX-154364698-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 3P and 5B. PP2PP3_ModerateBP6BS2
The NM_001110556.2(FLNA):c.1850C>T(p.Ser617Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000911 in 1,207,897 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. S617S) 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNA | NM_001110556.2 | c.1850C>T | p.Ser617Leu | missense_variant | 13/48 | ENST00000369850.10 | |
FLNA | NM_001456.4 | c.1850C>T | p.Ser617Leu | missense_variant | 13/47 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNA | ENST00000369850.10 | c.1850C>T | p.Ser617Leu | missense_variant | 13/48 | 1 | NM_001110556.2 |
Frequencies
GnomAD3 genomes AF: 0.00000905 AC: 1AN: 110534Hom.: 0 Cov.: 24 AF XY: 0.0000306 AC XY: 1AN XY: 32732
GnomAD3 exomes AF: 0.0000331 AC: 6AN: 181120Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67134
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1097363Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 3AN XY: 362977
GnomAD4 genome AF: 0.00000905 AC: 1AN: 110534Hom.: 0 Cov.: 24 AF XY: 0.0000306 AC XY: 1AN XY: 32732
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 13, 2021 | Has not been previously published as pathogenic or benign to our knowledge; Reported in ClinVar as a variant of uncertain significance (ClinVar Variant ID# 190185; Landrum et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26582918, 27535533) - |
Heterotopia, periventricular, X-linked dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Claritas Genomics | Oct 03, 2013 | - - |
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 | Nov 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at