11-5689947-A-G

Variant names:

• chr11-5689947-A-G
• rs7129909
• NM_006074.5:c.-67+48A>G

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+48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,136 control chromosomes in the GnomAD database, including 7,681 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 0.32 (7675 hom., cov: 32)
  • Exomes 𝑓: 0.35 (6 hom.)
• Consequence: TRIM22 NM_006074.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 16 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]

ENSG00000295362 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.427 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM22	NM_006074.5	MANE Select	c.-67+48A>G		intron	N/A	NP_006065.2
	TRIM22	NM_001199573.2		c.-67+48A>G		intron	N/A	NP_001186502.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM22	ENST00000379965.8	TSL:1 MANE Select	c.-67+48A>G		intron	N/A	ENSP00000369299.3
	TRIM5	ENST00000412903.1	TSL:1	c.-61-9709T>C		intron	N/A	ENSP00000388031.1
	TRIM22	ENST00000454828.6	TSL:5	c.-67+48A>G		intron	N/A	ENSP00000393250.2

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48056 AN: 151930 Hom.: 7679 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.350

GnomAD4 exome AF: 0.352 AC: 31 AN: 88 Hom.: 6 Cov.: 0 AF XY: 0.324 AC XY: 22 AN XY: 68

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.348 AC: 23 AN: 66

Other (OTH) AF: 0.417 AC: 5 AN: 12

GnomAD4 genome AF: 0.316 AC: 48077 AN: 152048 Hom.: 7675 Cov.: 32 AF XY: 0.317 AC XY: 23551 AN XY: 74300

African (AFR) AF: 0.254 AC: 10519 AN: 41468

American (AMR) AF: 0.280 AC: 4280 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3470

East Asian (EAS) AF: 0.314 AC: 1623 AN: 5164

South Asian (SAS) AF: 0.443 AC: 2138 AN: 4826

European-Finnish (FIN) AF: 0.320 AC: 3385 AN: 10570

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23895 AN: 67968

Other (OTH) AF: 0.350 AC: 740 AN: 2114

Alfa AF: 0.344 Hom.: 7166

Bravo AF: 0.308

Asia WGS AF: 0.359 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.7
DANN	Benign	0.77
PhyloP100		-0.38
PromoterAI		0.030	Neutral
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: rs7129909; hg19: chr11-5711177;