chr11-5701877-G-C

Variant names:

• chr11-5701877-G-C
• rs2179
• NM_006074.5:c.750+3332G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TRIM22	NM_006074.5	c.750+3332G>C		intron_variant	Intron 4 of 7	ENST00000379965.8	NP_006065.2
TRIM22	NM_001199573.2	c.738+3332G>C		intron_variant	Intron 4 of 7		NP_001186502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM22	ENST00000379965.8	c.750+3332G>C		intron_variant	Intron 4 of 7	1	NM_006074.5	ENSP00000369299.3

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

African (AFR) AF: 0.826 AC: 34256 AN: 41448

American (AMR) AF: 0.787 AC: 12014 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2550 AN: 3472

East Asian (EAS) AF: 0.603 AC: 3104 AN: 5148

South Asian (SAS) AF: 0.672 AC: 3238 AN: 4818

European-Finnish (FIN) AF: 0.657 AC: 6899 AN: 10496

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.712 AC: 48378 AN: 67932

Other (OTH) AF: 0.754 AC: 1586 AN: 2104

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
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2179; hg19: chr11-5723107;