11-5666794-G-C

Variant names:

• chr11-5666794-G-C
• rs11820502
• NM_033034.3:c.768-713C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033034.3(TRIM5):​c.768-713C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 152,184 control chromosomes in the GnomAD database, including 19,277 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 0.46 (19277 hom., cov: 33)
• Consequence: TRIM5 NM_033034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963
• Publications: 7 publications found

Genes affected

TRIM5 (HGNC:16276): (tripartite motif containing 5) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. 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. The protein forms homo-oligomers via the coilel-coil region and localizes to cytoplasmic bodies. It appears to function as a E3 ubiquitin-ligase and ubiqutinates itself to regulate its subcellular localization. It may play a role in retroviral restriction. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2009]

ENSG00000239920 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033034.3. 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
	TRIM5	NM_033034.3	MANE Select	c.768-713C>G		intron	N/A	NP_149023.2
	TRIM5	NM_033092.4		c.768-713C>G		intron	N/A	NP_149083.2
	TRIM5	NM_033093.4		c.768-713C>G		intron	N/A	NP_149084.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIM5	ENST00000380034.8	TSL:2 MANE Select	c.768-713C>G		intron	N/A	ENSP00000369373.3
	TRIM5	ENST00000396847.7	TSL:1	c.768-713C>G		intron	N/A	ENSP00000380058.3
	ENSG00000239920	ENST00000380259.7	TSL:5	n.231+11410C>G		intron	N/A	ENSP00000369609.3

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69259 AN: 152066 Hom.: 19216 Cov.: 33

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.406

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.456 AC: 69400 AN: 152184 Hom.: 19277 Cov.: 33 AF XY: 0.455 AC XY: 33834 AN XY: 74398

African (AFR) AF: 0.771 AC: 32040 AN: 41546

American (AMR) AF: 0.471 AC: 7196 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1137 AN: 3472

East Asian (EAS) AF: 0.605 AC: 3134 AN: 5176

South Asian (SAS) AF: 0.382 AC: 1844 AN: 4826

European-Finnish (FIN) AF: 0.279 AC: 2946 AN: 10578

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19803 AN: 67980

Other (OTH) AF: 0.407 AC: 861 AN: 2114

Alfa AF: 0.215 Hom.: 474

Bravo AF: 0.490

Asia WGS AF: 0.506 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.96
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: rs11820502; hg19: chr11-5688024;