rs2179

chr11-5701877-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006074.5(TRIM22):c.750+3332G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 151,876 control chromosomes in the GnomAD database, including 42,515 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.74 (42515 hom., cov: 31)
• Consequence: TRIM22 NM_006074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM22	NM_006074.5	c.750+3332G>C		intron_variant		ENST00000379965.8
TRIM22	NM_001199573.2	c.738+3332G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM22	ENST00000379965.8	c.750+3332G>C		intron_variant		1	NM_006074.5	P1

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112897 AN: 151758 Hom.: 42470 Cov.: 31

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.757

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.744 AC: 112999 AN: 151876 Hom.: 42515 Cov.: 31 AF XY: 0.740 AC XY: 54882 AN XY: 74198

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.754

Alfa AF: 0.726 Hom.: 5006

Bravo AF: 0.755

Asia WGS AF: 0.698 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.42

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

Other links and lift over

dbSNP: rs2179; hg19: chr11-5723107;