rs150162389
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003902.5(FUBP1):āc.1588A>Gā(p.Thr530Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000762 in 1,612,048 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Genomes: š 0.0041 ( 3 hom., cov: 32)
Exomes š: 0.00041 ( 7 hom. )
Consequence
FUBP1
NM_003902.5 missense
NM_003902.5 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 4.21
Genes affected
FUBP1 (HGNC:4004): (far upstream element binding protein 1) The protein encoded by this gene is a single stranded DNA-binding protein that binds to multiple DNA elements, including the far upstream element (FUSE) located upstream of c-myc. Binding to FUSE occurs on the non-coding strand, and is important to the regulation of c-myc in undifferentiated cells. This protein contains three domains, an amphipathic helix N-terminal domain, a DNA-binding central domain, and a C-terminal transactivation domain that contains three tyrosine-rich motifs. The N-terminal domain is thought to repress the activity of the C-terminal domain. This protein is also thought to bind RNA, and contains 3'-5' helicase activity with in vitro activity on both DNA-DNA and RNA-RNA duplexes. Aberrant expression of this gene has been found in malignant tissues, and this gene is important to neural system and lung development. Binding of this protein to viral RNA is thought to play a role in several viral diseases, including hepatitis C and hand, foot and mouth disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0072716475).
BS2
?
High AC in GnomAd4 at 628 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUBP1 | NM_003902.5 | c.1588A>G | p.Thr530Ala | missense_variant | 17/20 | ENST00000370768.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUBP1 | ENST00000370768.7 | c.1588A>G | p.Thr530Ala | missense_variant | 17/20 | 1 | NM_003902.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00412 AC: 626AN: 152044Hom.: 3 Cov.: 32
GnomAD3 genomes
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32
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GnomAD3 exomes AF: 0.00114 AC: 286AN: 251180Hom.: 1 AF XY: 0.000869 AC XY: 118AN XY: 135784
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GnomAD4 exome AF: 0.000411 AC: 600AN: 1459886Hom.: 7 Cov.: 29 AF XY: 0.000336 AC XY: 244AN XY: 726308
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GnomAD4 genome ? AF: 0.00413 AC: 628AN: 152162Hom.: 3 Cov.: 32 AF XY: 0.00405 AC XY: 301AN XY: 74392
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ExAC
?
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176
Asia WGS
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3478
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at