Variant 8-66150348-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_184085.2(TRIM55):c.867G>A(p.Ser289=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 1,614,004 control chromosomes in the GnomAD database, including 2,823 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.082 ( 835 hom., cov: 33)

Exomes 𝑓: 0.045 ( 1988 hom. )

Consequence

TRIM55
NM_184085.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.171

Variant links:

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]

TRIM55 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 8-66150348-G-A is Benign according to our data. Variant chr8-66150348-G-A is described in ClinVar as [Benign]. Clinvar id is 3058969.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.171 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRIM55	NM_184085.2 linkuse as main transcript	c.867G>A	p.Ser289=	synonymous_variant	7/10	ENST00000315962.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIM55	ENST00000315962.9 linkuse as main transcript	c.867G>A	p.Ser289=	synonymous_variant	7/10	1	NM_184085.2	A1	Q9BYV6-1
TRIM55	ENST00000276573.11 linkuse as main transcript	c.867G>A	p.Ser289=	synonymous_variant	7/11	1		A1	Q9BYV6-3
TRIM55	ENST00000353317.9 linkuse as main transcript	c.867G>A	p.Ser289=	synonymous_variant	7/9	1		P4	Q9BYV6-2
TRIM55	ENST00000350034.4 linkuse as main transcript	c.603+13158G>A		intron_variant		1			Q9BYV6-4

Frequencies

GnomAD3 genomes

AF:

0.0821

AC:

12483

AN:

152046

Hom.:

834

Cov.:

show subpopulations

Gnomad AFR

AF:

0.181

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0492

Gnomad ASJ

AF:

0.0424

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0232

Gnomad FIN

AF:

0.0609

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0469

Gnomad OTH

AF:

0.0683

GnomAD3 exomes

AF:

0.0469

AC:

11789

AN:

251162

Hom.:

458

AF XY:

0.0447

AC XY:

6067

AN XY:

135748

show subpopulations

Gnomad AFR exome

AF:

0.180

Gnomad AMR exome

AF:

0.0267

Gnomad ASJ exome

AF:

0.0435

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0246

Gnomad FIN exome

AF:

0.0591

Gnomad NFE exome

AF:

0.0459

Gnomad OTH exome

AF:

0.0405

GnomAD4 exome

AF:

0.0454

AC:

66335

AN:

1461840

Hom.:

1988

Cov.:

AF XY:

0.0444

AC XY:

32258

AN XY:

727210

show subpopulations

Gnomad4 AFR exome

AF:

0.181

Gnomad4 AMR exome

AF:

0.0291

Gnomad4 ASJ exome

AF:

0.0409

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0252

Gnomad4 FIN exome

AF:

0.0576

Gnomad4 NFE exome

AF:

0.0445

Gnomad4 OTH exome

AF:

0.0492

GnomAD4 genome

AF:

0.0821

AC:

12494

AN:

152164

Hom.:

835

Cov.:

AF XY:

0.0805

AC XY:

5990

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.0490

Gnomad4 ASJ

AF:

0.0424

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0232

Gnomad4 FIN

AF:

0.0609

Gnomad4 NFE

AF:

0.0469

Gnomad4 OTH

AF:

0.0676

Alfa

AF:

0.0663

Hom.:

268

Bravo

AF:

0.0843

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TRIM55-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 22, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

8.2

DANN

Benign

0.55

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over