3-58008671-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 3P and 9B. PM1PP2BP4_StrongBP6BS1
The NM_001457.4(FLNB):c.107G>A(p.Arg36His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000418 in 1,614,156 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 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. R36L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001457.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNB | NM_001457.4 | c.107G>A | p.Arg36His | missense_variant | 1/46 | ENST00000295956.9 | |
FLNB | NM_001164317.2 | c.107G>A | p.Arg36His | missense_variant | 1/47 | ||
FLNB | NM_001164318.2 | c.107G>A | p.Arg36His | missense_variant | 1/46 | ||
FLNB | NM_001164319.2 | c.107G>A | p.Arg36His | missense_variant | 1/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNB | ENST00000295956.9 | c.107G>A | p.Arg36His | missense_variant | 1/46 | 1 | NM_001457.4 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00229 AC: 348AN: 152212Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000561 AC: 141AN: 251346Hom.: 0 AF XY: 0.000434 AC XY: 59AN XY: 135896
GnomAD4 exome AF: 0.000224 AC: 328AN: 1461826Hom.: 3 Cov.: 31 AF XY: 0.000195 AC XY: 142AN XY: 727228
GnomAD4 genome ? AF: 0.00228 AC: 347AN: 152330Hom.: 1 Cov.: 33 AF XY: 0.00211 AC XY: 157AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 01, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 24, 2016 | - - |
FLNB-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 12, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Connective tissue disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Aug 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at