Variant 11-5698558-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006074.5(TRIM22):c.750+13A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,600,324 control chromosomes in the GnomAD database, including 19,891 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 2815 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17076 hom. )

Consequence

TRIM22
NM_006074.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.162

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]

TRIM22 links:

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]

TRIM5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 11-5698558-A-G is Benign according to our data. Variant chr11-5698558-A-G is described in ClinVar as [Benign]. Clinvar id is 2688343.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM22	NM_006074.5 linkuse as main transcript	c.750+13A>G		intron_variant		ENST00000379965.8
TRIM22	NM_001199573.2 linkuse as main transcript	c.738+13A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM22	ENST00000379965.8 linkuse as main transcript	c.750+13A>G		intron_variant		1	NM_006074.5	P1	Q8IYM9-1

Frequencies

GnomAD3 genomes

AF:

0.178

AC:

27038

AN:

151956

Hom.:

2813

Cov.:

show subpopulations

Gnomad AFR

AF:

0.282

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.000386

Gnomad SAS

AF:

0.0443

Gnomad FIN

AF:

0.162

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.158

GnomAD3 exomes

AF:

0.129

AC:

30822

AN:

238326

Hom.:

2485

AF XY:

0.125

AC XY:

16123

AN XY:

129134

show subpopulations

Gnomad AFR exome

AF:

0.298

Gnomad AMR exome

AF:

0.0771

Gnomad ASJ exome

AF:

0.137

Gnomad EAS exome

AF:

0.000402

Gnomad SAS exome

AF:

0.0455

Gnomad FIN exome

AF:

0.165

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.138

GnomAD4 exome

AF:

0.147

AC:

212178

AN:

1448250

Hom.:

17076

Cov.:

AF XY:

0.143

AC XY:

102806

AN XY:

719310

show subpopulations

Gnomad4 AFR exome

AF:

0.289

Gnomad4 AMR exome

AF:

0.0816

Gnomad4 ASJ exome

AF:

0.139

Gnomad4 EAS exome

AF:

0.000228

Gnomad4 SAS exome

AF:

0.0478

Gnomad4 FIN exome

AF:

0.169

Gnomad4 NFE exome

AF:

0.157

Gnomad4 OTH exome

AF:

0.147

GnomAD4 genome

AF:

0.178

AC:

27052

AN:

152074

Hom.:

2815

Cov.:

AF XY:

0.173

AC XY:

12852

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.282

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.000580

Gnomad4 SAS

AF:

0.0446

Gnomad4 FIN

AF:

0.162

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.156

Alfa

AF:

0.164

Hom.:

587

Bravo

AF:

0.180

Asia WGS

AF:

0.0370

AC:

132

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 20% of patients studied by a panel of primary immunodeficiencies. Number of patients: 19. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.2

DANN

Benign

0.79

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over