1-63323186-G-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4
The NM_012183.3(FOXD3):c.128G>A(p.Gly43Asp) 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
FOXD3
NM_012183.3 missense
NM_012183.3 missense
Scores
2
3
13
Clinical Significance
Conservation
PhyloP100: 1.09
Publications
0 publications found
Genes affected
FOXD3 (HGNC:3804): (forkhead box D3) This gene belongs to the forkhead family of transcription factors which is characterized by a distinct forkhead domain. Mutations in this gene cause autoimmune susceptibility 1. [provided by RefSeq, Nov 2008]
FOXD3-AS1 (HGNC:40241): (FOXD3 antisense RNA 1)
ENSG00000293613 (HGNC:):
ITGB3BP (HGNC:6157): (integrin subunit beta 3 binding protein) This gene encodes a transcriptional coregulator that binds to and enhances the activity of members of the nuclear receptor families, thyroid hormone receptors and retinoid X receptors. This protein also acts as a corepressor of NF-kappaB-dependent signaling. This protein induces apoptosis in breast cancer cells through a caspase 2-mediated signaling pathway. This protein is also a component of the centromere-specific histone H3 variant nucleosome associated complex (CENP-NAC) and may be involved in mitotic progression by recruiting the histone H3 variant CENP-A to the centromere. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29749972).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012183.3. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1404896Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 694858
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1404896
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
694858
African (AFR)
AF:
AC:
0
AN:
30416
American (AMR)
AF:
AC:
0
AN:
37344
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24846
East Asian (EAS)
AF:
AC:
0
AN:
35190
South Asian (SAS)
AF:
AC:
0
AN:
79978
European-Finnish (FIN)
AF:
AC:
0
AN:
47488
Middle Eastern (MID)
AF:
AC:
0
AN:
5632
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1085724
Other (OTH)
AF:
AC:
0
AN:
58278
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of catalytic residue at A42 (P = 0.0625)
MVP
ClinPred
T
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
Publications
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