chr2-27305636-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_187841.3(TRIM54):​c.662G>A​(p.Cys221Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000649 in 1,613,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00042 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00067 ( 0 hom. )

Consequence

TRIM54
NM_187841.3 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.602
Variant links:
Genes affected
TRIM54 (HGNC:16008): (tripartite motif containing 54) The protein encoded by this gene contains a RING finger motif and is highly similar to the ring finger proteins RNF28/MURF1 and RNF29/MURF2. In vitro studies demonstrated that this protein, RNF28, and RNF29 form heterodimers, which may be important for the regulation of titin kinase and microtubule-dependent signal pathways in striated muscles. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.012906343).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TRIM54NM_187841.3 linkc.662G>A p.Cys221Tyr missense_variant Exon 5 of 9 ENST00000380075.7 NP_912730.2 Q9BYV2-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TRIM54ENST00000380075.7 linkc.662G>A p.Cys221Tyr missense_variant Exon 5 of 9 1 NM_187841.3 ENSP00000369415.3 Q9BYV2-1
TRIM54ENST00000296098.4 linkc.788G>A p.Cys263Tyr missense_variant Exon 6 of 10 1 ENSP00000296098.4 Q9BYV2-2
TRIM54ENST00000485306.1 linkn.452G>A non_coding_transcript_exon_variant Exon 1 of 3 2
TRIM54ENST00000488321.1 linkn.417G>A non_coding_transcript_exon_variant Exon 2 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.000420
AC:
64
AN:
152236
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000823
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000606
AC:
151
AN:
249188
Hom.:
0
AF XY:
0.000533
AC XY:
72
AN XY:
134958
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000869
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000512
Gnomad NFE exome
AF:
0.00119
Gnomad OTH exome
AF:
0.000656
GnomAD4 exome
AF:
0.000673
AC:
984
AN:
1461438
Hom.:
0
Cov.:
31
AF XY:
0.000604
AC XY:
439
AN XY:
727026
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000470
Gnomad4 NFE exome
AF:
0.000836
Gnomad4 OTH exome
AF:
0.000364
GnomAD4 genome
AF:
0.000420
AC:
64
AN:
152236
Hom.:
0
Cov.:
32
AF XY:
0.000390
AC XY:
29
AN XY:
74364
show subpopulations
Gnomad4 AFR
AF:
0.000121
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.000823
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000795
Hom.:
0
Bravo
AF:
0.000431
TwinsUK
AF:
0.000809
AC:
3
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00105
AC:
9
ExAC
AF:
0.000791
AC:
96
EpiCase
AF:
0.000545
EpiControl
AF:
0.000771

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jul 02, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.788G>A (p.C263Y) alteration is located in exon 6 (coding exon 6) of the TRIM54 gene. This alteration results from a G to A substitution at nucleotide position 788, causing the cysteine (C) at amino acid position 263 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.53
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
18
DANN
Benign
0.77
DEOGEN2
Benign
0.098
T;.
Eigen
Benign
-0.73
Eigen_PC
Benign
-0.52
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.84
T;T
M_CAP
Benign
0.0050
T
MetaRNN
Benign
0.013
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-1.1
N;.
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
4.4
N;N
REVEL
Benign
0.10
Sift
Benign
1.0
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0
B;B
Vest4
0.27
MVP
0.33
MPC
0.25
ClinPred
0.015
T
GERP RS
4.9
Varity_R
0.097
gMVP
0.36

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

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

Other links and lift over

dbSNP: rs41288823; hg19: chr2-27528504; API