3-58120049-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001457.4(FLNB):c.2863+1060C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,154 control chromosomes in the GnomAD database, including 4,087 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.20 ( 4087 hom., cov: 32)
Consequence
FLNB
NM_001457.4 intron
NM_001457.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00900
Publications
8 publications found
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]
FLNB Gene-Disease associations (from GenCC):
- atelosteogenesis type IInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
- atelosteogenesis type IIIInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
- Larsen syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
- spondylocarpotarsal synostosis syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
- Boomerang dysplasiaInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLNB | NM_001457.4 | c.2863+1060C>T | intron_variant | Intron 19 of 45 | ENST00000295956.9 | NP_001448.2 | ||
FLNB | NM_001164317.2 | c.2863+1060C>T | intron_variant | Intron 19 of 46 | NP_001157789.1 | |||
FLNB | NM_001164318.2 | c.2863+1060C>T | intron_variant | Intron 19 of 45 | NP_001157790.1 | |||
FLNB | NM_001164319.2 | c.2863+1060C>T | intron_variant | Intron 19 of 44 | NP_001157791.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.205 AC: 31133AN: 152036Hom.: 4079 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
31133
AN:
152036
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.205 AC: 31148AN: 152154Hom.: 4087 Cov.: 32 AF XY: 0.201 AC XY: 14977AN XY: 74384 show subpopulations
GnomAD4 genome
AF:
AC:
31148
AN:
152154
Hom.:
Cov.:
32
AF XY:
AC XY:
14977
AN XY:
74384
show subpopulations
African (AFR)
AF:
AC:
2872
AN:
41538
American (AMR)
AF:
AC:
2646
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
AC:
1224
AN:
3468
East Asian (EAS)
AF:
AC:
122
AN:
5180
South Asian (SAS)
AF:
AC:
866
AN:
4812
European-Finnish (FIN)
AF:
AC:
2624
AN:
10580
Middle Eastern (MID)
AF:
AC:
96
AN:
294
European-Non Finnish (NFE)
AF:
AC:
20054
AN:
67968
Other (OTH)
AF:
AC:
489
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1192
2384
3577
4769
5961
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
316
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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