rs35926783

Positions:

• chr11-5690561-A-G

Variant summary

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

The ENST00000379965.8(TRIM22):​c.-67+662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 152,210 control chromosomes in the GnomAD database, including 547 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 0.081 (547 hom., cov: 32)
• Consequence: TRIM22 ENST00000379965.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

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]

LOC124902620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM22	NM_006074.5	c.-67+662A>G		intron_variant		ENST00000379965.8	NP_006065.2
LOC124902620	XR_007062561.1	n.2077+117T>C		intron_variant, non_coding_transcript_variant
TRIM22	NM_001199573.2	c.-67+662A>G		intron_variant			NP_001186502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM22	ENST00000379965.8	c.-67+662A>G		intron_variant		1	NM_006074.5	ENSP00000369299	P1

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12326 AN: 152092 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0763

Gnomad ASJ AF: 0.0936

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0870

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0811 AC: 12346 AN: 152210 Hom.: 547 Cov.: 32 AF XY: 0.0790 AC XY: 5877 AN XY: 74424

Gnomad4 AFR AF: 0.0847

Gnomad4 AMR AF: 0.0762

Gnomad4 ASJ AF: 0.0936

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0869

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.0829 Hom.: 80

Bravo AF: 0.0821

Asia WGS AF: 0.0200 AC: 68 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.62

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: rs35926783; hg19: chr11-5711791;