11-120132825-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012101.4(TRIM29):​c.805-4330G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,172 control chromosomes in the GnomAD database, including 1,896 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1896 hom., cov: 33)

Consequence

TRIM29
NM_012101.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.101

Publications

8 publications found
Variant links:
Genes affected
TRIM29 (HGNC:17274): (tripartite motif containing 29) The protein encoded by this gene belongs to the TRIM protein family. It has multiple zinc finger motifs and a leucine zipper motif. It has been proposed to form homo- or heterodimers which are involved in nucleic acid binding. Thus, it may act as a transcriptional regulatory factor involved in carcinogenesis and/or differentiation. It may also function in the suppression of radiosensitivity since it is associated with ataxia telangiectasia phenotype. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIM29NM_012101.4 linkc.805-4330G>A intron_variant Intron 1 of 8 ENST00000341846.10 NP_036233.2 Q14134-1A0A024R3J1
TRIM29XM_047426688.1 linkc.805-4330G>A intron_variant Intron 1 of 9 XP_047282644.1
TRIM29XM_047426689.1 linkc.805-4330G>A intron_variant Intron 1 of 9 XP_047282645.1
LOC105369529XR_948100.3 linkn.197+4135C>T intron_variant Intron 1 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIM29ENST00000341846.10 linkc.805-4330G>A intron_variant Intron 1 of 8 1 NM_012101.4 ENSP00000343129.5 Q14134-1
TRIM29ENST00000475051.4 linkn.*143-4330G>A intron_variant Intron 2 of 9 5 ENSP00000433779.1 E9PJD4

Frequencies

GnomAD3 genomes
AF:
0.144
AC:
21916
AN:
152054
Hom.:
1896
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.180
Gnomad AMI
AF:
0.0943
Gnomad AMR
AF:
0.133
Gnomad ASJ
AF:
0.0960
Gnomad EAS
AF:
0.443
Gnomad SAS
AF:
0.106
Gnomad FIN
AF:
0.139
Gnomad MID
AF:
0.0854
Gnomad NFE
AF:
0.110
Gnomad OTH
AF:
0.125
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.144
AC:
21928
AN:
152172
Hom.:
1896
Cov.:
33
AF XY:
0.146
AC XY:
10847
AN XY:
74378
show subpopulations
African (AFR)
AF:
0.180
AC:
7452
AN:
41502
American (AMR)
AF:
0.133
AC:
2036
AN:
15288
Ashkenazi Jewish (ASJ)
AF:
0.0960
AC:
333
AN:
3470
East Asian (EAS)
AF:
0.444
AC:
2294
AN:
5172
South Asian (SAS)
AF:
0.104
AC:
502
AN:
4818
European-Finnish (FIN)
AF:
0.139
AC:
1473
AN:
10596
Middle Eastern (MID)
AF:
0.0884
AC:
26
AN:
294
European-Non Finnish (NFE)
AF:
0.110
AC:
7464
AN:
68010
Other (OTH)
AF:
0.124
AC:
262
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
973
1946
2919
3892
4865
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
242
484
726
968
1210
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.120
Hom.:
5820
Bravo
AF:
0.150
Asia WGS
AF:
0.240
AC:
832
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
6.3
DANN
Benign
0.67
PhyloP100
0.10
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs666432; hg19: chr11-120003533; API