rs80356520
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_001457.4(FLNB):āc.4819C>Gā(p.Arg1607Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FLNB
NM_001457.4 missense
NM_001457.4 missense
Scores
8
10
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.09
Genes affected
FLNB (HGNC:3755): (filamin B) This gene encodes a member of the filamin family. The encoded protein interacts with glycoprotein Ib alpha as part of the process to repair vascular injuries. The platelet glycoprotein Ib complex includes glycoprotein Ib alpha, and it binds the actin cytoskeleton. Mutations in this gene have been found in several conditions: atelosteogenesis type 1 and type 3; boomerang dysplasia; autosomal dominant Larsen syndrome; and spondylocarpotarsal synostosis syndrome. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM1
In a repeat Filamin 14 (size 96) in uniprot entity FLNB_HUMAN there are 15 pathogenic changes around while only 0 benign (100%) in NM_001457.4
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.868
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FLNB | NM_001457.4 | c.4819C>G | p.Arg1607Gly | missense_variant | Exon 28 of 46 | ENST00000295956.9 | NP_001448.2 | |
| FLNB | NM_001164317.2 | c.4912C>G | p.Arg1638Gly | missense_variant | Exon 29 of 47 | NP_001157789.1 | ||
| FLNB | NM_001164318.2 | c.4819C>G | p.Arg1607Gly | missense_variant | Exon 28 of 46 | NP_001157790.1 | ||
| FLNB | NM_001164319.2 | c.4819C>G | p.Arg1607Gly | missense_variant | Exon 28 of 45 | NP_001157791.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1461600Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727118
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1461600
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
727118
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ExAC
AF:
AC:
4
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Pathogenic
.;D;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
.;M;M;M;.
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D
Polyphen
0.81, 0.78, 0.62
.;P;P;.;P
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at