17-38945127-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001008777.3(FBXO47):​c.626A>C​(p.Gln209Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q209R) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 30)

Consequence

FBXO47
NM_001008777.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.10
Variant links:
Genes affected
FBXO47 (HGNC:31969): (F-box protein 47)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.10850713).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FBXO47NM_001008777.3 linkc.626A>C p.Gln209Pro missense_variant 7/11 ENST00000378079.3 NP_001008777.2 Q5MNV8
FBXO47XM_011524865.3 linkc.548A>C p.Gln183Pro missense_variant 7/11 XP_011523167.1
FBXO47XM_011524866.4 linkc.455A>C p.Gln152Pro missense_variant 6/10 XP_011523168.1
FBXO47XM_011524867.3 linkc.626A>C p.Gln209Pro missense_variant 7/10 XP_011523169.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FBXO47ENST00000378079.3 linkc.626A>C p.Gln209Pro missense_variant 7/111 NM_001008777.3 ENSP00000367319.2 Q5MNV8

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.084
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.44
CADD
Benign
17
DANN
Benign
0.94
DEOGEN2
Benign
0.0041
T
Eigen
Benign
-0.69
Eigen_PC
Benign
-0.49
FATHMM_MKL
Benign
0.69
D
LIST_S2
Benign
0.11
T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.11
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N
PrimateAI
Uncertain
0.56
T
PROVEAN
Benign
-0.23
N
REVEL
Benign
0.034
Sift
Benign
0.42
T
Sift4G
Benign
0.21
T
Polyphen
0.031
B
Vest4
0.24
MutPred
0.42
Gain of loop (P = 0.0079);
MVP
0.23
MPC
0.083
ClinPred
0.11
T
GERP RS
3.5
Varity_R
0.13
gMVP
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9906595; hg19: chr17-37101380; API