NM_012204.4:c.127C>T
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012204.4(GTF3C4):c.127C>T(p.Pro43Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000217 in 1,382,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000022 ( 0 hom. )
Consequence
GTF3C4
NM_012204.4 missense
NM_012204.4 missense
Scores
4
2
12
Clinical Significance
Conservation
PhyloP100: 3.65
Publications
0 publications found
Genes affected
GTF3C4 (HGNC:4667): (general transcription factor IIIC subunit 4) Predicted to enable enzyme activator activity. Predicted to contribute to DNA binding activity. Predicted to be involved in 5S class rRNA transcription by RNA polymerase III and tRNA transcription by RNA polymerase III. Located in mitochondrion and nucleoplasm. Part of transcription factor TFIIIC complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.16552508).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012204.4. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GTF3C4 | TSL:1 MANE Select | c.127C>T | p.Pro43Ser | missense | Exon 1 of 5 | ENSP00000361219.4 | Q9UKN8 | ||
| GTF3C4 | c.127C>T | p.Pro43Ser | missense | Exon 1 of 5 | ENSP00000568904.1 | ||||
| GTF3C4 | TSL:3 | c.127C>T | p.Pro43Ser | missense | Exon 1 of 3 | ENSP00000431378.1 | F2Z356 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000217 AC: 3AN: 1382616Hom.: 0 Cov.: 33 AF XY: 0.00000439 AC XY: 3AN XY: 682868 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1382616
Hom.:
Cov.:
33
AF XY:
AC XY:
3
AN XY:
682868
show subpopulations
African (AFR)
AF:
AC:
0
AN:
30876
American (AMR)
AF:
AC:
0
AN:
35208
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24834
East Asian (EAS)
AF:
AC:
0
AN:
35220
South Asian (SAS)
AF:
AC:
0
AN:
79278
European-Finnish (FIN)
AF:
AC:
0
AN:
35312
Middle Eastern (MID)
AF:
AC:
0
AN:
4404
European-Non Finnish (NFE)
AF:
AC:
3
AN:
1079804
Other (OTH)
AF:
AC:
0
AN:
57680
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
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
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
B
Vest4
MutPred
Gain of phosphorylation at P43 (P = 0.0269)
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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