Genetic Variant TRIM22:p.His100His (chr11-5696532-T-C) – ACMG Classification: Benign (-15 pts)

Variant summary

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

The NM_006074.5(TRIM22):c.300T>C(p.His100His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 1,613,852 control chromosomes in the GnomAD database, including 193,939 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.46 ( 16203 hom., cov: 33)

Exomes 𝑓: 0.49 ( 177736 hom. )

Consequence

TRIM22
NM_006074.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.762

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=-0.63).

BP6

Variant 11-5696532-T-C is Benign according to our data. Variant chr11-5696532-T-C is described in ClinVar as [Benign]. Clinvar id is 2687989.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.762 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM22	NM_006074.5 link	c.300T>C	p.His100His	synonymous_variant	Exon 2 of 8	ENST00000379965.8	NP_006065.2	Q8IYM9-1B4DQS5
TRIM22	NM_001199573.2 link	c.300T>C	p.His100His	synonymous_variant	Exon 2 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.300T>C	p.His100His	synonymous_variant	Exon 2 of 8	1	NM_006074.5	ENSP00000369299.3		Q8IYM9-1

Frequencies

GnomAD3 genomes

AF:

0.456

AC:

69231

AN:

151894

Hom.:

16196

Cov.:

show subpopulations

Gnomad AFR

AF:

0.394

Gnomad AMI

AF:

0.509

Gnomad AMR

AF:

0.446

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.486

Gnomad FIN

AF:

0.482

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.506

Gnomad OTH

AF:

0.457

GnomAD3 exomes

AF:

0.453

AC:

113283

AN:

249944

Hom.:

27064

AF XY:

0.461

AC XY:

62515

AN XY:

135576

show subpopulations

Gnomad AFR exome

AF:

0.388

Gnomad AMR exome

AF:

0.349

Gnomad ASJ exome

AF:

0.552

Gnomad EAS exome

AF:

0.178

Gnomad SAS exome

AF:

0.493

Gnomad FIN exome

AF:

0.487

Gnomad NFE exome

AF:

0.511

Gnomad OTH exome

AF:

0.478

GnomAD4 exome

AF:

0.489

AC:

714591

AN:

1461840

Hom.:

177736

Cov.:

AF XY:

0.490

AC XY:

356011

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.396

Gnomad4 AMR exome

AF:

0.359

Gnomad4 ASJ exome

AF:

0.544

Gnomad4 EAS exome

AF:

0.198

Gnomad4 SAS exome

AF:

0.490

Gnomad4 FIN exome

AF:

0.493

Gnomad4 NFE exome

AF:

0.506

Gnomad4 OTH exome

AF:

0.478

GnomAD4 genome

AF:

0.456

AC:

69279

AN:

152012

Hom.:

16203

Cov.:

AF XY:

0.453

AC XY:

33627

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.394

Gnomad4 AMR

AF:

0.446

Gnomad4 ASJ

AF:

0.539

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.487

Gnomad4 FIN

AF:

0.482

Gnomad4 NFE

AF:

0.506

Gnomad4 OTH

AF:

0.457

Alfa

AF:

0.495

Hom.:

23915

Bravo

AF:

0.442

EpiCase

AF:

0.500

EpiControl

AF:

0.509

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 75% of patients studied by a panel of primary immunodeficiencies. Number of patients: 71. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.63

CADD

Benign

7.8

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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