chr11-6448827-G-A

Variant names:

• chr11-6448827-G-A
• rs2723636
• ENST00000533064.1:n.1440C>T

Variant summary

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

The ENST00000533064.1(TRIM3):​n.1440C>T variant causes a non coding transcript exon 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 ENST00000533064.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.38
• Publications: 13 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=-0.41).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533064.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM3	NM_033278.4	MANE Select	c.*201C>T		3_prime_UTR	Exon 12 of 12	NP_150594.2
	TRIM3	NM_001248006.2		c.*201C>T		3_prime_UTR	Exon 12 of 12	NP_001234935.1
	TRIM3	NM_006458.4		c.*201C>T		3_prime_UTR	Exon 13 of 13	NP_006449.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM3	ENST00000533064.1	TSL:1	n.1440C>T		non_coding_transcript_exon	Exon 2 of 2
	TRIM3	ENST00000345851.8	TSL:1 MANE Select	c.*201C>T		3_prime_UTR	Exon 12 of 12	ENSP00000340797.3
	TRIM3	ENST00000532542.1	TSL:2	n.4209C>T		non_coding_transcript_exon	Exon 2 of 2

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

GnomAD2 exomes AF: 0.166 AC: 13526 AN: 81322 AF XY: 0.166

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 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

African (AFR) AF: 0.261 AC: 3586 AN: 13728

American (AMR) AF: 0.143 AC: 3250 AN: 22676

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 3477 AN: 14754

East Asian (EAS) AF: 0.0303 AC: 952 AN: 31424

South Asian (SAS) AF: 0.191 AC: 9494 AN: 49774

European-Finnish (FIN) AF: 0.140 AC: 4391 AN: 31410

Middle Eastern (MID) AF: 0.171 AC: 524 AN: 3060

European-Non Finnish (NFE) AF: 0.178 AC: 53910 AN: 303312

Other (OTH) AF: 0.176 AC: 4936 AN: 28032

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

African (AFR) AF: 0.260 AC: 10752 AN: 41348

American (AMR) AF: 0.162 AC: 2476 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3470

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5156

South Asian (SAS) AF: 0.189 AC: 910 AN: 4822

European-Finnish (FIN) AF: 0.139 AC: 1467 AN: 10590

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12211 AN: 67958

Other (OTH) AF: 0.176 AC: 369 AN: 2102

Alfa AF: 0.182 Hom.: 5158

Bravo AF: 0.197

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	18
DANN	Benign	0.87
PhyloP100		2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2723636; hg19: chr11-6470057;