ENST00000412903.1:c.-61-39166C>T

Variant names:

• chr11-5719404-G-A
• rs12285602
• ENST00000412903.1:c.-61-39166C>T

Variant summary

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

The ENST00000412903.1(TRIM5):​c.-61-39166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,034 control chromosomes in the GnomAD database, including 2,321 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 0.15 (2320 hom., cov: 32)
  • Exomes 𝑓: 0.071 (1 hom.)
• Consequence: TRIM5 ENST00000412903.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.69
• Publications: 3 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]

OR52U1P (HGNC:15237): (olfactory receptor family 52 subfamily U member 1 pseudogene) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

TRIM22 (HGNC:16379): (tripartite motif containing 22) 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. This protein localizes to the cytoplasm and its expression is induced by interferon. The protein is involved in innate immunity against different DNA and RNA viruses. [provided by RefSeq, Oct 2021]

TRIM22 Gene-Disease associations (from GenCC):

• inflammatory bowel disease

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OR52U1P		n.5719404G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM5	ENST00000412903.1	c.-61-39166C>T		intron_variant	Intron 2 of 4	1		ENSP00000388031.1
OR52U1P	ENST00000439752.1	n.115G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
TRIM5	ENST00000380027.5	c.-440-34010C>T		intron_variant	Intron 3 of 10	5		ENSP00000369366.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23219 AN: 151860 Hom.: 2311 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.0699

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0860

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.0714 AC: 4 AN: 56 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 38

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0455 AC: 1 AN: 22

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.0938 AC: 3 AN: 32

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.153 AC: 23280 AN: 151978 Hom.: 2320 Cov.: 32 AF XY: 0.154 AC XY: 11408 AN XY: 74290

African (AFR) AF: 0.271 AC: 11213 AN: 41406

American (AMR) AF: 0.199 AC: 3035 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 226 AN: 3466

East Asian (EAS) AF: 0.208 AC: 1076 AN: 5176

South Asian (SAS) AF: 0.0696 AC: 335 AN: 4814

European-Finnish (FIN) AF: 0.111 AC: 1175 AN: 10566

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0860 AC: 5841 AN: 67954

Other (OTH) AF: 0.139 AC: 293 AN: 2112

Alfa AF: 0.109 Hom.: 4008

Bravo AF: 0.169

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.061
DANN	Benign	0.67
PhyloP100		-4.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs12285602; hg19: chr11-5740634;