chr11-5698021-T-C

Variant names:

• chr11-5698021-T-C
• rs10769180
• NM_006074.5:c.520-294T>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.520-294T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 310,332 control chromosomes in the GnomAD database, including 76,245 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 0.69 (36757 hom., cov: 32)
  • Exomes 𝑓: 0.70 (39488 hom.)
• Consequence: TRIM22 NM_006074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM22	NM_006074.5	c.520-294T>C		intron_variant	Intron 3 of 7	ENST00000379965.8	NP_006065.2
TRIM22	NM_001199573.2	c.520-306T>C		intron_variant	Intron 3 of 7		NP_001186502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM22	ENST00000379965.8	c.520-294T>C		intron_variant	Intron 3 of 7	1	NM_006074.5	ENSP00000369299.3

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105444 AN: 151972 Hom.: 36725 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.700

GnomAD4 exome AF: 0.701 AC: 110941 AN: 158242 Hom.: 39488 Cov.: 2 AF XY: 0.712 AC XY: 59455 AN XY: 83456

African (AFR) AF: 0.726 AC: 4222 AN: 5812

American (AMR) AF: 0.728 AC: 6595 AN: 9054

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2873 AN: 4404

East Asian (EAS) AF: 0.778 AC: 7497 AN: 9634

South Asian (SAS) AF: 0.834 AC: 18017 AN: 21592

European-Finnish (FIN) AF: 0.674 AC: 4125 AN: 6118

Middle Eastern (MID) AF: 0.706 AC: 456 AN: 646

European-Non Finnish (NFE) AF: 0.664 AC: 61239 AN: 92226

Other (OTH) AF: 0.676 AC: 5917 AN: 8756

GnomAD4 genome AF: 0.694 AC: 105540 AN: 152090 Hom.: 36757 Cov.: 32 AF XY: 0.697 AC XY: 51838 AN XY: 74344

African (AFR) AF: 0.731 AC: 30327 AN: 41462

American (AMR) AF: 0.680 AC: 10389 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2246 AN: 3470

East Asian (EAS) AF: 0.760 AC: 3929 AN: 5172

South Asian (SAS) AF: 0.830 AC: 4008 AN: 4828

European-Finnish (FIN) AF: 0.679 AC: 7183 AN: 10574

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45083 AN: 67982

Other (OTH) AF: 0.701 AC: 1478 AN: 2108

Alfa AF: 0.675 Hom.: 59957

Bravo AF: 0.697

Asia WGS AF: 0.789 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.39
PhyloP100		-1.4
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: rs10769180; hg19: chr11-5719251;