7-73313249-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_178125.3(TRIM50):c.1136C>T(p.Ser379Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000553 in 1,446,494 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
TRIM50
NM_178125.3 missense
NM_178125.3 missense
Scores
12
5
Clinical Significance
Conservation
PhyloP100: 0.908
Genes affected
TRIM50 (HGNC:19017): (tripartite motif containing 50) Enables identical protein binding activity. Predicted to be involved in protein ubiquitination. Predicted to act upstream of or within regulation of establishment of protein localization. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM50 | NM_178125.3 | c.1136C>T | p.Ser379Phe | missense_variant | 7/7 | ENST00000333149.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM50 | ENST00000333149.7 | c.1136C>T | p.Ser379Phe | missense_variant | 7/7 | 1 | NM_178125.3 | P1 | |
TRIM50 | ENST00000453152.1 | c.1136C>T | p.Ser379Phe | missense_variant | 7/7 | 2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000906 AC: 2AN: 220802Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 119356
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GnomAD4 exome AF: 0.00000553 AC: 8AN: 1446494Hom.: 0 Cov.: 31 AF XY: 0.00000279 AC XY: 2AN XY: 718070
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 26, 2023 | The c.1136C>T (p.S379F) alteration is located in exon 7 (coding exon 6) of the TRIM50 gene. This alteration results from a C to T substitution at nucleotide position 1136, causing the serine (S) at amino acid position 379 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Uncertain
T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Uncertain
D;D
Vest4
MutPred
Loss of disorder (P = 0.0045);Loss of disorder (P = 0.0045);
MVP
MPC
ClinPred
D
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at