rs11607224

Variant names:

• chr11-6473685-G-A
• rs11607224
• NM_033278.4:c.-38+106C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_006458.4(TRIM3):​c.-203+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_006458.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 6 publications found

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]

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006458.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM3	NM_033278.4	MANE Select	c.-38+106C>T		intron	N/A	NP_150594.2
	TRIM3	NM_001248006.2		c.-38+417C>T		intron	N/A	NP_001234935.1
	TRIM3	NM_006458.4		c.-203+106C>T		intron	N/A	NP_006449.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM3	ENST00000345851.8	TSL:1 MANE Select	c.-38+106C>T		intron	N/A	ENSP00000340797.3
	TRIM3	ENST00000359518.7	TSL:5	c.-203+106C>T		intron	N/A	ENSP00000352508.3
	TRIM3	ENST00000525074.5	TSL:2	c.-38+417C>T		intron	N/A	ENSP00000433102.1

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.100 AC: 22 AN: 220

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.270 AC: 20 AN: 74

Other (OTH) AF: 0.300 AC: 3 AN: 10

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

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: 64 AN: 290

European-Non Finnish (NFE) AF: 0.173 AC: 11746 AN: 67924

Other (OTH) AF: 0.174 AC: 367 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.97
PhyloP100		0.42
PromoterAI		-0.0062	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11607224; hg19: chr11-6494915;