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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000380259.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000239920	ENST00000380259.7	TSL:5	n.231+15867C>T		intron	N/A	ENSP00000369609.3	A0A2U3TZJ3
	ENSG00000239920	ENST00000642298.1		n.151+3319C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7122620;

hg19: chr11-5683567;