rs11607224

Positions:

• chr11-6473685-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.-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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419

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=-0.46).
• 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/exons	MANE	Protein	UniProt
TRIM3	NM_033278.4	c.-38+106C>T		intron_variant		ENST00000345851.8	NP_150594.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIM3	ENST00000345851.8	c.-38+106C>T		intron_variant		1	NM_033278.4	ENSP00000340797.3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26162 AN: 151882 Hom.: 2330 Cov.: 31

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: 46 AN: 310 Hom.: 1 AF XY: 0.169 AC XY: 30 AN XY: 178

Gnomad4 AFR exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.270

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.172 AC: 26180 AN: 152000 Hom.: 2336 Cov.: 31 AF XY: 0.169 AC XY: 12569 AN XY: 74294

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.0256

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.174

Alfa AF: 0.172 Hom.: 301

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	16
DANN	Benign	0.97

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

LitVar

Other links and lift over

dbSNP: rs11607224; hg19: chr11-6494915;