11-5696550-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_006074.5(TRIM22):c.318C>T(p.Ile106=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,614,230 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0051 (1 hom., cov: 33)
  • Exomes 𝑓: 0.0012 (7 hom.)
• Consequence: TRIM22 NM_006074.5 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.03

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]

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]

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BP6: Variant 11-5696550-C-T is Benign according to our data. Variant chr11-5696550-C-T is described in ClinVar as [Benign]. Clinvar id is 713987.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-1.03 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM22	NM_006074.5	c.318C>T	p.Ile106=	synonymous_variant	2/8	ENST00000379965.8
TRIM22	NM_001199573.2	c.318C>T	p.Ile106=	synonymous_variant	2/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM22	ENST00000379965.8	c.318C>T	p.Ile106=	synonymous_variant	2/8	1	NM_006074.5	P1

Frequencies

GnomAD3 genomes AF: 0.00513 AC: 781 AN: 152226 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00693

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000749

Gnomad OTH AF: 0.0105

GnomAD3 exomes AF: 0.00222 AC: 554 AN: 249894 Hom.: 1 AF XY: 0.00187 AC XY: 254 AN XY: 135570

Gnomad AFR exome AF: 0.0149

Gnomad AMR exome AF: 0.00426

Gnomad ASJ exome AF: 0.00497

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000935

Gnomad OTH exome AF: 0.00297

GnomAD4 exome AF: 0.00124 AC: 1808 AN: 1461886 Hom.: 7 Cov.: 33 AF XY: 0.00115 AC XY: 834 AN XY: 727244

Gnomad4 AFR exome AF: 0.0141

Gnomad4 AMR exome AF: 0.00438

Gnomad4 ASJ exome AF: 0.00643

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000128

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000673

Gnomad4 OTH exome AF: 0.00291

GnomAD4 genome AF: 0.00513 AC: 782 AN: 152344 Hom.: 1 Cov.: 33 AF XY: 0.00497 AC XY: 370 AN XY: 74500

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.00692

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000750

Gnomad4 OTH AF: 0.0104

Alfa AF: 0.00376 Hom.: 1

Bravo AF: 0.00634

Asia WGS AF: 0.000866 AC: 3 AN: 3478

EpiCase AF: 0.00142

EpiControl AF: 0.00148

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jun 14, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	7.8
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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

Other links and lift over

dbSNP: rs61735271; hg19: chr11-5717780;