11-5698437-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_006074.5(TRIM22):c.642T>C(p.Asp214Asp) 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

Publications

23 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIM22	NM_006074.5 link	c.642T>C	p.Asp214Asp	synonymous_variant	Exon 4 of 8	ENST00000379965.8	NP_006065.2	Q8IYM9-1B4DQS5
TRIM22	NM_001199573.2 link	c.630T>C	p.Asp210Asp	synonymous_variant	Exon 4 of 8		NP_001186502.1	Q8IYM9-2B4DQS5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM22	ENST00000379965.8 link	c.642T>C	p.Asp214Asp	synonymous_variant	Exon 4 of 8	1	NM_006074.5	ENSP00000369299.3		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

GnomAD2 exomes

AF:

0.252

AC:

62934

AN:

249448

AF XY:

0.251

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 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

African (AFR)

AF:

0.323

AC:

10799

AN:

33468

American (AMR)

AF:

0.358

AC:

16024

AN:

44708

Ashkenazi Jewish (ASJ)

AF:

0.275

AC:

7193

AN:

26136

East Asian (EAS)

AF:

0.338

AC:

13399

AN:

39696

South Asian (SAS)

AF:

0.320

AC:

27643

AN:

86252

European-Finnish (FIN)

AF:

0.156

AC:

8332

AN:

53420

Middle Eastern (MID)

AF:

0.320

AC:

1838

AN:

5738

European-Non Finnish (NFE)

AF:

0.192

AC:

213629

AN:

1111936

Other (OTH)

AF:

0.232

AC:

14022

AN:

60378

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

13796

27592

41387

55183

68979

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7716

15432

23148

30864

38580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.246

AC:

37501

AN:

152148

Hom.:

4920

Cov.:

AF XY:

0.248

AC XY:

18478

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.316

AC:

13133

AN:

41500

American (AMR)

AF:

0.302

AC:

4620

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

933

AN:

3472

East Asian (EAS)

AF:

0.310

AC:

1604

AN:

5166

South Asian (SAS)

AF:

0.319

AC:

1538

AN:

4824

European-Finnish (FIN)

AF:

0.152

AC:

1608

AN:

10588

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.194

AC:

13197

AN:

67994

Other (OTH)

AF:

0.255

AC:

540

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1485

2970

4454

5939

7424

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

394

788

1182

1576

1970

<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:

0.222

Hom.:

6441

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

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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

(source)

DANN

Benign

0.83

PhyloP100

-0.24

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over