rs7122620

Variant names:

• chr11-5662337-G-A
• rs7122620
• ENST00000380259.7:n.231+15867C>T

Variant summary

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

The ENST00000380259.7(ENSG00000239920):​n.231+15867C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,064 control chromosomes in the GnomAD database, including 19,593 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 0.50 (19593 hom., cov: 32)
• Consequence: ENSG00000239920 ENST00000380259.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 11 publications found

Genes affected

ENSG00000239920 (HGNC:):

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM5	XM_047427783.1	c.794+3319C>T		intron_variant	Intron 6 of 6		XP_047283739.1
TRIM5	XM_047427784.1	c.744+15867C>T		intron_variant	Intron 4 of 4		XP_047283740.1
TRIM5	XR_001748014.3	n.1163+3319C>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000239920	ENST00000380259.7	n.231+15867C>T		intron_variant	Intron 1 of 7	5		ENSP00000369609.3
ENSG00000239920	ENST00000642298.1	n.151+3319C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75717 AN: 151946 Hom.: 19590 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.498 AC: 75747 AN: 152064 Hom.: 19593 Cov.: 32 AF XY: 0.489 AC XY: 36374 AN XY: 74320

African (AFR) AF: 0.476 AC: 19719 AN: 41458

American (AMR) AF: 0.444 AC: 6783 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1865 AN: 3472

East Asian (EAS) AF: 0.116 AC: 598 AN: 5174

South Asian (SAS) AF: 0.307 AC: 1482 AN: 4824

European-Finnish (FIN) AF: 0.550 AC: 5822 AN: 10578

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37798 AN: 67970

Other (OTH) AF: 0.503 AC: 1061 AN: 2108

Alfa AF: 0.532 Hom.: 37123

Bravo AF: 0.491

Asia WGS AF: 0.293 AC: 1019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs7122620; hg19: chr11-5683567;