rs6537825

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_015906.4(TRIM33):ā€‹c.2519T>Cā€‹(p.Ile840Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 1,614,150 control chromosomes in the GnomAD database, including 684,209 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: š‘“ 0.92 ( 64802 hom., cov: 32)
Exomes š‘“: 0.92 ( 619407 hom. )

Consequence

TRIM33
NM_015906.4 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.04
Variant links:
Genes affected
TRIM33 (HGNC:16290): (tripartite motif containing 33) The protein encoded by this gene is thought to be a transcriptional corepressor. However, molecules that interact with this protein have not yet been identified. The protein is a member of the tripartite motif family. This motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. Three alternatively spliced transcript variants for this gene have been described, however, the full-length nature of one variant has not been determined. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=5.423833E-7).
BP6
Variant 1-114405659-A-G is Benign according to our data. Variant chr1-114405659-A-G is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TRIM33NM_015906.4 linkuse as main transcriptc.2519T>C p.Ile840Thr missense_variant 15/20 ENST00000358465.7 NP_056990.3 Q9UPN9-1B3KN30

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TRIM33ENST00000358465.7 linkuse as main transcriptc.2519T>C p.Ile840Thr missense_variant 15/201 NM_015906.4 ENSP00000351250.2 Q9UPN9-1
TRIM33ENST00000369543.6 linkuse as main transcriptc.2519T>C p.Ile840Thr missense_variant 15/191 ENSP00000358556.2 Q9UPN9-2
TRIM33ENST00000448034.5 linkuse as main transcriptc.1799T>C p.Ile600Thr missense_variant 13/185 ENSP00000402333.1 H0Y612
TRIM33ENST00000476908.1 linkuse as main transcriptn.128T>C non_coding_transcript_exon_variant 2/22

Frequencies

GnomAD3 genomes
AF:
0.919
AC:
139880
AN:
152152
Hom.:
64745
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.970
Gnomad AMI
AF:
0.912
Gnomad AMR
AF:
0.839
Gnomad ASJ
AF:
0.888
Gnomad EAS
AF:
0.597
Gnomad SAS
AF:
0.915
Gnomad FIN
AF:
0.966
Gnomad MID
AF:
0.801
Gnomad NFE
AF:
0.928
Gnomad OTH
AF:
0.885
GnomAD3 exomes
AF:
0.885
AC:
222458
AN:
251428
Hom.:
99797
AF XY:
0.890
AC XY:
120959
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.971
Gnomad AMR exome
AF:
0.774
Gnomad ASJ exome
AF:
0.890
Gnomad EAS exome
AF:
0.596
Gnomad SAS exome
AF:
0.921
Gnomad FIN exome
AF:
0.965
Gnomad NFE exome
AF:
0.927
Gnomad OTH exome
AF:
0.888
GnomAD4 exome
AF:
0.919
AC:
1342815
AN:
1461880
Hom.:
619407
Cov.:
65
AF XY:
0.919
AC XY:
668340
AN XY:
727242
show subpopulations
Gnomad4 AFR exome
AF:
0.972
Gnomad4 AMR exome
AF:
0.780
Gnomad4 ASJ exome
AF:
0.890
Gnomad4 EAS exome
AF:
0.644
Gnomad4 SAS exome
AF:
0.919
Gnomad4 FIN exome
AF:
0.964
Gnomad4 NFE exome
AF:
0.932
Gnomad4 OTH exome
AF:
0.898
GnomAD4 genome
AF:
0.919
AC:
139994
AN:
152270
Hom.:
64802
Cov.:
32
AF XY:
0.917
AC XY:
68252
AN XY:
74450
show subpopulations
Gnomad4 AFR
AF:
0.970
Gnomad4 AMR
AF:
0.838
Gnomad4 ASJ
AF:
0.888
Gnomad4 EAS
AF:
0.598
Gnomad4 SAS
AF:
0.916
Gnomad4 FIN
AF:
0.966
Gnomad4 NFE
AF:
0.928
Gnomad4 OTH
AF:
0.884
Alfa
AF:
0.916
Hom.:
161338
Bravo
AF:
0.907
TwinsUK
AF:
0.926
AC:
3432
ALSPAC
AF:
0.936
AC:
3607
ESP6500AA
AF:
0.971
AC:
4280
ESP6500EA
AF:
0.927
AC:
7976
ExAC
AF:
0.892
AC:
108296
Asia WGS
AF:
0.794
AC:
2761
AN:
3478
EpiCase
AF:
0.916
EpiControl
AF:
0.916

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.041
BayesDel_addAF
Benign
-0.54
T
BayesDel_noAF
Benign
-0.41
CADD
Benign
17
DANN
Benign
0.30
DEOGEN2
Benign
0.045
T;.
Eigen
Benign
-0.78
Eigen_PC
Benign
-0.50
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.062
T;T
MetaRNN
Benign
5.4e-7
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-2.0
N;N
PrimateAI
Benign
0.46
T
PROVEAN
Benign
2.3
N;N
REVEL
Benign
0.10
Sift
Benign
1.0
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0
B;B
Vest4
0.024
MPC
0.66
ClinPred
0.0029
T
GERP RS
4.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.021
gMVP
0.21

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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: rs6537825; hg19: chr1-114948281; COSMIC: COSV61821233; API