rs205499

chr17-56895040-G-A

Variant summary

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

The NM_005082.5(TRIM25):c.1363+303C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,164 control chromosomes in the GnomAD database, including 2,599 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 0.18 (2599 hom., cov: 32)
• Consequence: TRIM25 NM_005082.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348

Genes affected

TRIM25 (HGNC:12932): (tripartite motif containing 25) 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 is an RNA binding protein, functions as a ubiquitin E3 ligase and is involved in multiple cellular processes, including regulation of antiviral innate immunity. [provided by RefSeq, Sep 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM25	NM_005082.5	c.1363+303C>T		intron_variant		ENST00000316881.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM25	ENST00000316881.9	c.1363+303C>T		intron_variant		1	NM_005082.5	P1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27249 AN: 152048 Hom.: 2603 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.179 AC: 27240 AN: 152164 Hom.: 2599 Cov.: 32 AF XY: 0.176 AC XY: 13107 AN XY: 74392

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.0125

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.196

Alfa AF: 0.198 Hom.: 4451

Bravo AF: 0.177

Asia WGS AF: 0.0660 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs205499; hg19: chr17-54972401;