dbSNP rs7129909: TRIM22:c.-67+48A>G (chr11-5689947-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.382

Publications

16 publications found

Variant links:

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]

TRIM22 links:

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]

TRIM5 links:

ENSG00000295362 (HGNC:):

ENSG00000295362 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM22	NM_006074.5 link	c.-67+48A>G		intron_variant	Intron 1 of 7	ENST00000379965.8	NP_006065.2
TRIM22	NM_001199573.2 link	c.-67+48A>G		intron_variant	Intron 1 of 7		NP_001186502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM22	ENST00000379965.8 link	c.-67+48A>G		intron_variant	Intron 1 of 7	1	NM_006074.5	ENSP00000369299.3

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

48056

AN:

151930

Hom.:

7679

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

0.324

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.348

AC:

AN:

Other (OTH)

AF:

0.417

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.316

AC:

48077

AN:

152048

Hom.:

7675

Cov.:

AF XY:

0.317

AC XY:

23551

AN XY:

74300

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.352

AC:

23895

AN:

67968

Other (OTH)

AF:

0.350

AC:

740

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1717

3434

5152

6869

8586

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.7

(source)

DANN

Benign

0.77

PhyloP100

-0.38

PromoterAI

0.030

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over