11-5891250-T-C

Variant summary

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

The ENST00000412903.1(TRIM5):c.-62+46151A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,730 control chromosomes in the GnomAD database, including 11,650 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 0.39 (11650 hom., cov: 30)
• Consequence: TRIM5 ENST00000412903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

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]

LOC112268071 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268071	XR_002957231.2	n.365-9821A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM5	ENST00000412903.1	c.-62+46151A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58634 AN: 151612 Hom.: 11647 Cov.: 30

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.387 AC: 58660 AN: 151730 Hom.: 11650 Cov.: 30 AF XY: 0.385 AC XY: 28531 AN XY: 74102

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.386

Alfa AF: 0.409 Hom.: 1556

Bravo AF: 0.380

Asia WGS AF: 0.352 AC: 1220 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.9
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463289; hg19: chr11-5912480;