NM_006074.5:c.-67+2688A>C

Variant names:

• chr11-5692587-A-C
• rs12294511
• NM_006074.5:c.-67+2688A>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.-67+2688A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,080 control chromosomes in the GnomAD database, including 13,010 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 0.41 (13010 hom., cov: 32)
• Consequence: TRIM22 NM_006074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 2 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]

LOC124902620 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006074.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM22	NM_006074.5	MANE Select	c.-67+2688A>C		intron	N/A	NP_006065.2	Q8IYM9-1
	TRIM22	NM_001199573.2		c.-67+2688A>C		intron	N/A	NP_001186502.1	Q8IYM9-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM22	ENST00000379965.8	TSL:1 MANE Select	c.-67+2688A>C		intron	N/A	ENSP00000369299.3	Q8IYM9-1
	TRIM5	ENST00000412903.1	TSL:1	c.-61-12349T>G		intron	N/A	ENSP00000388031.1	E7EQQ5
	TRIM22	ENST00000901728.1		c.-59+2688A>C		intron	N/A	ENSP00000571787.1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61982 AN: 151962 Hom.: 13003 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.408 AC: 62027 AN: 152080 Hom.: 13010 Cov.: 32 AF XY: 0.404 AC XY: 30026 AN XY: 74336

African (AFR) AF: 0.333 AC: 13821 AN: 41486

American (AMR) AF: 0.408 AC: 6237 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3470

East Asian (EAS) AF: 0.179 AC: 926 AN: 5174

South Asian (SAS) AF: 0.324 AC: 1566 AN: 4830

European-Finnish (FIN) AF: 0.451 AC: 4758 AN: 10558

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31557 AN: 67950

Other (OTH) AF: 0.417 AC: 881 AN: 2114

Alfa AF: 0.354 Hom.: 1990

Bravo AF: 0.397

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.54
PhyloP100		0.0010
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: rs12294511; hg19: chr11-5713817;