chr11-6448827-G-A

Position:

• chr11-6448827-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_033278.4(TRIM3):​c.*201C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 650,086 control chromosomes in the GnomAD database, including 10,923 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 0.19 (3126 hom., cov: 32)
  • Exomes 𝑓: 0.17 (7797 hom.)
• Consequence: TRIM3 NM_033278.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.38

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIM3	NM_033278.4	c.*201C>T		3_prime_UTR_variant	12/12	ENST00000345851.8	NP_150594.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM3	ENST00000345851	c.*201C>T		3_prime_UTR_variant	12/12	1	NM_033278.4	ENSP00000340797.3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29291 AN: 151798 Hom.: 3119 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0153

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.178

GnomAD3 exomes AF: 0.166 AC: 13526 AN: 81322 Hom.: 1309 AF XY: 0.166 AC XY: 6877 AN XY: 41432

Gnomad AFR exome AF: 0.263

Gnomad AMR exome AF: 0.145

Gnomad ASJ exome AF: 0.252

Gnomad EAS exome AF: 0.0137

Gnomad SAS exome AF: 0.198

Gnomad FIN exome AF: 0.152

Gnomad NFE exome AF: 0.182

Gnomad OTH exome AF: 0.175

GnomAD4 exome AF: 0.170 AC: 84520 AN: 498170 Hom.: 7797 Cov.: 6 AF XY: 0.171 AC XY: 44910 AN XY: 261902

Gnomad4 AFR exome AF: 0.261

Gnomad4 AMR exome AF: 0.143

Gnomad4 ASJ exome AF: 0.236

Gnomad4 EAS exome AF: 0.0303

Gnomad4 SAS exome AF: 0.191

Gnomad4 FIN exome AF: 0.140

Gnomad4 NFE exome AF: 0.178

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.193 AC: 29320 AN: 151916 Hom.: 3126 Cov.: 32 AF XY: 0.190 AC XY: 14146 AN XY: 74258

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.176

Alfa AF: 0.181 Hom.: 3736

Bravo AF: 0.197

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.87

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

Other links and lift over

dbSNP: rs2723636; hg19: chr11-6470057;