rs10769180

chr11-5698021-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
TRIM22	NM_006074.5	c.520-294T>C		intron_variant		ENST00000379965.8
TRIM22	NM_001199573.2	c.520-306T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM22	ENST00000379965.8	c.520-294T>C		intron_variant		1	NM_006074.5	P1

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

Gnomad4 AFR exome AF: 0.726

Gnomad4 AMR exome AF: 0.728

Gnomad4 ASJ exome AF: 0.652

Gnomad4 EAS exome AF: 0.778

Gnomad4 SAS exome AF: 0.834

Gnomad4 FIN exome AF: 0.674

Gnomad4 NFE exome AF: 0.664

Gnomad4 OTH exome AF: 0.676

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

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.680

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.701

Alfa AF: 0.673 Hom.: 47572

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

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: rs10769180; hg19: chr11-5719251;