11-5698437-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_006074.5(TRIM22):c.642T>C(p.Asp214=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,613,880 control chromosomes in the GnomAD database, including 40,692 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 4920 hom., cov: 33)

Exomes 𝑓: 0.21 ( 35772 hom. )

Consequence

TRIM22
NM_006074.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.243

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 11-5698437-T-C is Benign according to our data. Variant chr11-5698437-T-C is described in ClinVar as [Benign]. Clinvar id is 2688112.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.243 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 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.642T>C	p.Asp214=	synonymous_variant	4/8	ENST00000379965.8
TRIM22	NM_001199573.2 linkuse as main transcript	c.630T>C	p.Asp210=	synonymous_variant	4/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM22	ENST00000379965.8 linkuse as main transcript	c.642T>C	p.Asp214=	synonymous_variant	4/8	1	NM_006074.5	P1	Q8IYM9-1

Frequencies

GnomAD3 genomes

AF:

0.246

AC:

37446

AN:

152030

Hom.:

4915

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.310

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.152

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.194

Gnomad OTH

AF:

0.258

GnomAD3 exomes

AF:

0.252

AC:

62934

AN:

249448

Hom.:

8744

AF XY:

0.251

AC XY:

33911

AN XY:

135336

show subpopulations

Gnomad AFR exome

AF:

0.321

Gnomad AMR exome

AF:

0.368

Gnomad ASJ exome

AF:

0.271

Gnomad EAS exome

AF:

0.299

Gnomad SAS exome

AF:

0.320

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.200

Gnomad OTH exome

AF:

0.235

GnomAD4 exome

AF:

0.214

AC:

312879

AN:

1461732

Hom.:

35772

Cov.:

AF XY:

0.217

AC XY:

157549

AN XY:

727164

show subpopulations

Gnomad4 AFR exome

AF:

0.323

Gnomad4 AMR exome

AF:

0.358

Gnomad4 ASJ exome

AF:

0.275

Gnomad4 EAS exome

AF:

0.338

Gnomad4 SAS exome

AF:

0.320

Gnomad4 FIN exome

AF:

0.156

Gnomad4 NFE exome

AF:

0.192

Gnomad4 OTH exome

AF:

0.232

GnomAD4 genome

AF:

0.246

AC:

37501

AN:

152148

Hom.:

4920

Cov.:

AF XY:

0.248

AC XY:

18478

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.302

Gnomad4 ASJ

AF:

0.269

Gnomad4 EAS

AF:

0.310

Gnomad4 SAS

AF:

0.319

Gnomad4 FIN

AF:

0.152

Gnomad4 NFE

AF:

0.194

Gnomad4 OTH

AF:

0.255

Alfa

AF:

0.221

Hom.:

5651

Bravo

AF:

0.259

Asia WGS

AF:

0.295

AC:

1024

AN:

3478

EpiCase

AF:

0.214

EpiControl

AF:

0.208

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 52% of patients studied by a panel of primary immunodeficiencies. Number of patients: 49. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

Cadd

Benign

0.75

Dann

Benign

0.83

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