rs1453424

Variant names:

• chr11-5796303-T-C
• rs1453424
• ENST00000412903.1:c.-61-116065A>G

Variant summary

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

The ENST00000412903.1(TRIM5):​c.-61-116065A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,824 control chromosomes in the GnomAD database, including 8,736 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 0.33 (8736 hom., cov: 31)
• Consequence: TRIM5 ENST00000412903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 0 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM5	ENST00000412903.1	c.-61-116065A>G		intron_variant	Intron 2 of 4	1		ENSP00000388031.1
TRIM5	ENST00000380027.5	c.-441+59449A>G		intron_variant	Intron 3 of 10	5		ENSP00000369366.1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50386 AN: 151708 Hom.: 8735 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.332 AC: 50427 AN: 151824 Hom.: 8736 Cov.: 31 AF XY: 0.330 AC XY: 24444 AN XY: 74184

African (AFR) AF: 0.439 AC: 18164 AN: 41416

American (AMR) AF: 0.304 AC: 4627 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3472

East Asian (EAS) AF: 0.207 AC: 1069 AN: 5172

South Asian (SAS) AF: 0.263 AC: 1268 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3115 AN: 10478

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20214 AN: 67918

Other (OTH) AF: 0.320 AC: 675 AN: 2110

Alfa AF: 0.306 Hom.: 3744

Bravo AF: 0.341

Asia WGS AF: 0.246 AC: 852 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		0.059
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1453424; hg19: chr11-5817533;