Variant rs16913748 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_033278.4(TRIM3):c.603C>T(p.Ile201Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,613,888 control chromosomes in the GnomAD database, including 31,799 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 0.21 ( 3535 hom., cov: 33)

Exomes 𝑓: 0.19 ( 28264 hom. )

Consequence

TRIM3
NM_033278.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.62

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:

TRIM3 (HGNC:):

TRIM3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP7

Synonymous conserved (PhyloP=1.62 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM3	NM_033278.4 linkuse as main transcript	c.603C>T	p.Ile201Ile	synonymous_variant	5/12	ENST00000345851.8	NP_150594.2	O75382-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM3	ENST00000345851.8 linkuse as main transcript	c.603C>T	p.Ile201Ile	synonymous_variant	5/12	1	NM_033278.4	ENSP00000340797.3		O75382-1

Frequencies

GnomAD3 genomes

AF:

0.207

AC:

31434

AN:

152124

Hom.:

3531

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.173

Gnomad ASJ

AF:

0.248

Gnomad EAS

AF:

0.0158

Gnomad SAS

AF:

0.226

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.195

Gnomad OTH

AF:

0.204

GnomAD3 exomes

AF:

0.179

AC:

45047

AN:

251218

Hom.:

4617

AF XY:

0.183

AC XY:

24869

AN XY:

135810

show subpopulations

Gnomad AFR exome

AF:

0.279

Gnomad AMR exome

AF:

0.137

Gnomad ASJ exome

AF:

0.237

Gnomad EAS exome

AF:

0.0151

Gnomad SAS exome

AF:

0.235

Gnomad FIN exome

AF:

0.131

Gnomad NFE exome

AF:

0.193

Gnomad OTH exome

AF:

0.193

GnomAD4 exome

AF:

0.192

AC:

280205

AN:

1461646

Hom.:

28264

Cov.:

AF XY:

0.194

AC XY:

140798

AN XY:

727124

show subpopulations

Gnomad4 AFR exome

AF:

0.280

Gnomad4 AMR exome

AF:

0.143

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.0231

Gnomad4 SAS exome

AF:

0.235

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.195

Gnomad4 OTH exome

AF:

0.198

GnomAD4 genome

AF:

0.207

AC:

31454

AN:

152242

Hom.:

3535

Cov.:

AF XY:

0.201

AC XY:

15000

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.280

Gnomad4 AMR

AF:

0.173

Gnomad4 ASJ

AF:

0.248

Gnomad4 EAS

AF:

0.0158

Gnomad4 SAS

AF:

0.226

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.195

Gnomad4 OTH

AF:

0.203

Alfa

AF:

0.203

Hom.:

4181

Bravo

AF:

0.212

Asia WGS

AF:

0.122

AC:

425

AN:

3478

EpiCase

AF:

0.202

EpiControl

AF:

0.210

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

8.6

DANN

Benign

0.83

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over