Genetic Variant TRIM3:c.-38+106C>T (chr11-6473685-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_033278.4(TRIM3):c.-38+106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,310 control chromosomes in the GnomAD database, including 2,337 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 0.17 ( 2336 hom., cov: 31)

Exomes 𝑓: 0.15 ( 1 hom. )

Consequence

TRIM3
NM_033278.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.419

Publications

6 publications found

Variant links:

Genes affected

TRIM3 (HGNC:10064): (tripartite motif containing 3) The protein encoded by this gene is a member of the tripartite motif (TRIM) family, also called the 'RING-B-box-coiled-coil' (RBCC) subgroup of RING finger proteins. 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 cytoplasmic filaments. It is similar to a rat protein which is a specific partner for the tail domain of myosin V, a class of myosins which are involved in the targeted transport of organelles. The rat protein can also interact with alpha-actinin-4. Thus it is suggested that this human protein may play a role in myosin V-mediated cargo transport. Alternatively spliced transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008]

TRIM3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM3	NM_033278.4 link	c.-38+106C>T		intron_variant	Intron 1 of 11	ENST00000345851.8	NP_150594.2	O75382-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM3	ENST00000345851.8 link	c.-38+106C>T		intron_variant	Intron 1 of 11	1	NM_033278.4	ENSP00000340797.3		O75382-1

Frequencies

GnomAD3 genomes

AF:

0.172

AC:

26162

AN:

151882

Hom.:

2330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.0255

Gnomad SAS

AF:

0.210

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.175

GnomAD4 exome

AF:

0.148

AC:

AN:

310

Hom.:

AF XY:

0.169

AC XY:

AN XY:

178

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.250

AC:

AN:

European-Finnish (FIN)

AF:

0.100

AC:

AN:

220

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.270

AC:

AN:

Other (OTH)

AF:

0.300

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.172

AC:

26180

AN:

152000

Hom.:

2336

Cov.:

AF XY:

0.169

AC XY:

12569

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.205

AC:

8493

AN:

41426

American (AMR)

AF:

0.153

AC:

2343

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.240

AC:

832

AN:

3468

East Asian (EAS)

AF:

0.0256

AC:

132

AN:

5158

South Asian (SAS)

AF:

0.211

AC:

1016

AN:

4820

European-Finnish (FIN)

AF:

0.103

AC:

1095

AN:

10604

Middle Eastern (MID)

AF:

0.221

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.173

AC:

11746

AN:

67924

Other (OTH)

AF:

0.174

AC:

367

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1082

2163

3245

4326

5408

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.174

Hom.:

311

Bravo

AF:

0.176

Asia WGS

AF:

0.116

AC:

406

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.97

PhyloP100

0.42

PromoterAI

-0.0062

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over