1-89011778-T-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_018284.3(GBP3):c.1118A>T(p.Asp373Val) 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 pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 26)
Exomes 𝑓: 0.0000015 ( 1 hom. )
Failed GnomAD Quality Control
Consequence
GBP3
NM_018284.3 missense
NM_018284.3 missense
Scores
5
6
7
Clinical Significance
Conservation
PhyloP100: 2.24
Publications
0 publications found
Genes affected
GBP3 (HGNC:4184): (guanylate binding protein 3) This gene encodes a member of the guanylate-binding protein (GBP) family. GBPs specifically bind guanine nucleotides (GMP, GDP, and GTP) and contain two of the three consensus motifs found in typical GTP-binding proteins. The encoded protein interacts with a member of the germinal center kinase family. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.874
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_018284.3. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GBP3 | TSL:1 MANE Select | c.1118A>T | p.Asp373Val | missense | Exon 7 of 11 | ENSP00000359512.4 | Q9H0R5-1 | ||
| GBP3 | TSL:1 | n.*928A>T | non_coding_transcript_exon | Exon 8 of 12 | ENSP00000456449.1 | H3BRX6 | |||
| GBP3 | TSL:1 | n.*928A>T | 3_prime_UTR | Exon 8 of 12 | ENSP00000456449.1 | H3BRX6 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
26
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000151 AC: 2AN: 1322662Hom.: 1 Cov.: 31 AF XY: 0.00000304 AC XY: 2AN XY: 658502 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2
AN:
1322662
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
658502
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33250
American (AMR)
AF:
AC:
0
AN:
42440
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
22708
East Asian (EAS)
AF:
AC:
0
AN:
38364
South Asian (SAS)
AF:
AC:
0
AN:
80460
European-Finnish (FIN)
AF:
AC:
0
AN:
50270
Middle Eastern (MID)
AF:
AC:
0
AN:
5314
European-Non Finnish (NFE)
AF:
AC:
0
AN:
994750
Other (OTH)
AF:
AC:
2
AN:
55106
GnomAD4 genome
GnomAD4 genome
Cov.:
26
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
Uncertain
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H
PhyloP100
PrimateAI
Benign
T
PROVEAN
Pathogenic
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Gain of MoRF binding (P = 0.0285)
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
DS_DG_spliceai
Position offset: 50
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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