rs2291842

Variant names:

• chr11-5698437-T-C
• rs2291842
• NM_006074.5:c.642T>C
• TRIM22 p.Asp214Asp

Your query was ambiguous. Multiple possible variants found:

• chr11-5698437-T-C
• chr11-5698437-T-A

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_006074.5(TRIM22):​c.642T>C​(p.Asp214Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,613,880 control chromosomes in the GnomAD database, including 40,692 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.25 (4920 hom., cov: 33)
  • Exomes 𝑓: 0.21 (35772 hom.)
• Consequence: TRIM22 NM_006074.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.243
• Publications: 23 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 -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 11-5698437-T-C is Benign according to our data. Variant chr11-5698437-T-C is described in ClinVar as Benign. ClinVar VariationId is 2688112.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.243 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.312 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.642T>C	p.Asp214Asp	synonymous	Exon 4 of 8	NP_006065.2	Q8IYM9-1
	TRIM22	NM_001199573.2		c.630T>C	p.Asp210Asp	synonymous	Exon 4 of 8	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.642T>C	p.Asp214Asp	synonymous	Exon 4 of 8	ENSP00000369299.3	Q8IYM9-1
	TRIM5	ENST00000412903.1	TSL:1	c.-61-18199A>G		intron	N/A	ENSP00000388031.1	E7EQQ5
	TRIM22	ENST00000901728.1		c.642T>C	p.Asp214Asp	synonymous	Exon 4 of 8	ENSP00000571787.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37446 AN: 152030 Hom.: 4915 Cov.: 33

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.258

GnomAD2 exomes AF: 0.252 AC: 62934 AN: 249448 AF XY: 0.251

Gnomad AFR exome AF: 0.321

Gnomad AMR exome AF: 0.368

Gnomad ASJ exome AF: 0.271

Gnomad EAS exome AF: 0.299

Gnomad FIN exome AF: 0.153

Gnomad NFE exome AF: 0.200

Gnomad OTH exome AF: 0.235

GnomAD4 exome AF: 0.214 AC: 312879 AN: 1461732 Hom.: 35772 Cov.: 33 AF XY: 0.217 AC XY: 157549 AN XY: 727164

African (AFR) AF: 0.323 AC: 10799 AN: 33468

American (AMR) AF: 0.358 AC: 16024 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 7193 AN: 26136

East Asian (EAS) AF: 0.338 AC: 13399 AN: 39696

South Asian (SAS) AF: 0.320 AC: 27643 AN: 86252

European-Finnish (FIN) AF: 0.156 AC: 8332 AN: 53420

Middle Eastern (MID) AF: 0.320 AC: 1838 AN: 5738

European-Non Finnish (NFE) AF: 0.192 AC: 213629 AN: 1111936

Other (OTH) AF: 0.232 AC: 14022 AN: 60378

GnomAD4 genome AF: 0.246 AC: 37501 AN: 152148 Hom.: 4920 Cov.: 33 AF XY: 0.248 AC XY: 18478 AN XY: 74384

African (AFR) AF: 0.316 AC: 13133 AN: 41500

American (AMR) AF: 0.302 AC: 4620 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1604 AN: 5166

South Asian (SAS) AF: 0.319 AC: 1538 AN: 4824

European-Finnish (FIN) AF: 0.152 AC: 1608 AN: 10588

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13197 AN: 67994

Other (OTH) AF: 0.255 AC: 540 AN: 2114

Alfa AF: 0.222 Hom.: 6441

Bravo AF: 0.259

Asia WGS AF: 0.295 AC: 1024 AN: 3478

EpiCase AF: 0.214

EpiControl AF: 0.208

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not specified (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.75
DANN	Benign	0.83
PhyloP100		-0.24
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2291842;

hg19: chr11-5719667;

COSMIC: COSV66090406;

COSMIC: COSV66090406;