8-66167360-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.235
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]

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ACMG classification

Classification made for transcript

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
TRIM55NM_184085.2 linkc.1525-7111C>T intron_variant Intron 9 of 9 ENST00000315962.9 NP_908973.1 Q9BYV6-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIM55ENST00000315962.9 linkc.1525-7111C>T intron_variant Intron 9 of 9 1 NM_184085.2 ENSP00000323913.4 Q9BYV6-1

Frequencies

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

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

Other links and lift over

dbSNP: rs7350113; hg19: chr8-67079595; API