Variant 11-5698605-T-C 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+60T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 1,358,996 control chromosomes in the GnomAD database, including 118,846 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 10551 hom., cov: 32)

Exomes 𝑓: 0.42 ( 108295 hom. )

Consequence

TRIM22
NM_006074.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.264

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 11-5698605-T-C is Benign according to our data. Variant chr11-5698605-T-C is described in ClinVar as [Benign]. Clinvar id is 2688019.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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+60T>C		intron_variant		ENST00000379965.8
TRIM22	NM_001199573.2 linkuse as main transcript	c.738+60T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM22	ENST00000379965.8 linkuse as main transcript	c.750+60T>C		intron_variant		1	NM_006074.5	P1	Q8IYM9-1

Frequencies

GnomAD3 genomes

AF:

0.342

AC:

52044

AN:

151956

Hom.:

10548

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.361

Gnomad EAS

AF:

0.651

Gnomad SAS

AF:

0.394

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.405

Gnomad OTH

AF:

0.361

GnomAD4 exome

AF:

0.419

AC:

505398

AN:

1206922

Hom.:

108295

AF XY:

0.418

AC XY:

250293

AN XY:

598456

show subpopulations

Gnomad4 AFR exome

AF:

0.126

Gnomad4 AMR exome

AF:

0.531

Gnomad4 ASJ exome

AF:

0.365

Gnomad4 EAS exome

AF:

0.663

Gnomad4 SAS exome

AF:

0.413

Gnomad4 FIN exome

AF:

0.423

Gnomad4 NFE exome

AF:

0.416

Gnomad4 OTH exome

AF:

0.406

GnomAD4 genome

AF:

0.342

AC:

52049

AN:

152074

Hom.:

10551

Cov.:

AF XY:

0.350

AC XY:

25986

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.361

Gnomad4 EAS

AF:

0.650

Gnomad4 SAS

AF:

0.396

Gnomad4 FIN

AF:

0.433

Gnomad4 NFE

AF:

0.405

Gnomad4 OTH

AF:

0.357

Alfa

AF:

0.388

Hom.:

14242

Bravo

AF:

0.336

Asia WGS

AF:

0.436

AC:

1513

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 69% of patients studied by a panel of primary immunodeficiencies. Number of patients: 66. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.2

DANN

Benign

0.67

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