8-66167360-C-T

Variant names:

• chr8-66167360-C-T
• rs7350113
• NM_184085.2:c.1525-7111C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_184085.2(TRIM55):​c.1525-7111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0254 in 152,224 control chromosomes in the GnomAD database, including 69 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 0.025 (69 hom., cov: 32)
• Consequence: TRIM55 NM_184085.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

TRIM55 (HGNC:14215): (tripartite motif containing 55) The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. This protein associates transiently with microtubules, myosin, and titin during muscle sarcomere assembly. It may act as a transient adaptor and plays a regulatory role in the assembly of sarcomeres. Four alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0254 (3860/152224) while in subpopulation NFE AF= 0.0409 (2779/67994). AF 95% confidence interval is 0.0396. There are 69 homozygotes in gnomad4. There are 1862 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 69 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIM55	NM_184085.2	c.1525-7111C>T		intron_variant	Intron 9 of 9	ENST00000315962.9	NP_908973.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIM55	ENST00000315962.9	c.1525-7111C>T		intron_variant	Intron 9 of 9	1	NM_184085.2	ENSP00000323913.4

Frequencies

GnomAD3 genomes AF: 0.0254 AC: 3861 AN: 152106 Hom.: 69 Cov.: 32

Gnomad AFR AF: 0.00683

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00539

Gnomad FIN AF: 0.0343

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0254 AC: 3860 AN: 152224 Hom.: 69 Cov.: 32 AF XY: 0.0250 AC XY: 1862 AN XY: 74426

Gnomad4 AFR AF: 0.00681

Gnomad4 AMR AF: 0.0192

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00539

Gnomad4 FIN AF: 0.0343

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0208

Alfa AF: 0.0129 Hom.: 5

Bravo AF: 0.0237

Asia WGS AF: 0.00375 AC: 13 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	3.7
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs7350113; hg19: chr8-67079595;