rs2179

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006074.5(TRIM22):​c.750+3332G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,876 control chromosomes in the GnomAD database, including 42,515 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 0.74 ( 42515 hom., cov: 31)

Consequence

TRIM22
NM_006074.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09
Variant links:
Genes affected
TRIM22 (HGNC:16379): (tripartite motif containing 22) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. This protein localizes to the cytoplasm and its expression is induced by interferon. The protein is involved in innate immunity against different DNA and RNA viruses. [provided by RefSeq, Oct 2021]
TRIM5 (HGNC:16276): (tripartite motif containing 5) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein forms homo-oligomers via the coilel-coil region and localizes to cytoplasmic bodies. It appears to function as a E3 ubiquitin-ligase and ubiqutinates itself to regulate its subcellular localization. It may play a role in retroviral restriction. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRIM22NM_006074.5 linkuse as main transcriptc.750+3332G>C intron_variant ENST00000379965.8
TRIM22NM_001199573.2 linkuse as main transcriptc.738+3332G>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRIM22ENST00000379965.8 linkuse as main transcriptc.750+3332G>C intron_variant 1 NM_006074.5 P1Q8IYM9-1

Frequencies

GnomAD3 genomes
AF:
0.744
AC:
112897
AN:
151758
Hom.:
42470
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.826
Gnomad AMI
AF:
0.820
Gnomad AMR
AF:
0.787
Gnomad ASJ
AF:
0.734
Gnomad EAS
AF:
0.603
Gnomad SAS
AF:
0.673
Gnomad FIN
AF:
0.657
Gnomad MID
AF:
0.793
Gnomad NFE
AF:
0.712
Gnomad OTH
AF:
0.757
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.744
AC:
112999
AN:
151876
Hom.:
42515
Cov.:
31
AF XY:
0.740
AC XY:
54882
AN XY:
74198
show subpopulations
Gnomad4 AFR
AF:
0.826
Gnomad4 AMR
AF:
0.787
Gnomad4 ASJ
AF:
0.734
Gnomad4 EAS
AF:
0.603
Gnomad4 SAS
AF:
0.672
Gnomad4 FIN
AF:
0.657
Gnomad4 NFE
AF:
0.712
Gnomad4 OTH
AF:
0.754
Alfa
AF:
0.726
Hom.:
5006
Bravo
AF:
0.755
Asia WGS
AF:
0.698
AC:
2429
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.6
DANN
Benign
0.42

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2179; hg19: chr11-5723107; API