rs1498553

Variant names:

• chr11-5687798-C-T
• rs1498553
• ENST00000412903.1:c.-61-7560G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412903.1(TRIM5):​c.-61-7560G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,910 control chromosomes in the GnomAD database, including 21,101 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 0.53 (21101 hom., cov: 32)
• Consequence: TRIM5 ENST00000412903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 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.-61-7560G>A		intron_variant	Intron 2 of 4	1		ENSP00000388031.1
TRIM5	ENST00000380027.5	c.-440-2404G>A		intron_variant	Intron 3 of 10	5		ENSP00000369366.1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79825 AN: 151794 Hom.: 21076 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.526 AC: 79901 AN: 151910 Hom.: 21101 Cov.: 32 AF XY: 0.526 AC XY: 39056 AN XY: 74218

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.502

Alfa AF: 0.528 Hom.: 5101

Bravo AF: 0.519

Asia WGS AF: 0.520 AC: 1805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1498553; hg19: chr11-5709028;