chr11-89799760-G-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_020358.2(TRIM49):āc.815C>Gā(p.Ala272Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0 ( 0 hom., cov: 21)
Exomes š: 0.000034 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TRIM49
NM_020358.2 missense
NM_020358.2 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: -0.0970
Genes affected
TRIM49 (HGNC:13431): (tripartite motif containing 49) The protein encoded by this gene contains a RING zinc finger, a motif known to be involved in protein-protein interactions. This gene has been found to be preferentially expressed in testis. Related pseudogenes and gene duplicates have also been identified on chromosome 11. [provided by RefSeq, Aug 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.09451738).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM49 | NM_020358.2 | c.815C>G | p.Ala272Gly | missense_variant | 7/8 | ENST00000329758.5 | |
TRIM49 | XM_017018027.3 | c.584C>G | p.Ala195Gly | missense_variant | 4/5 | ||
TRIM49 | XM_024448617.2 | c.738+1942C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM49 | ENST00000329758.5 | c.815C>G | p.Ala272Gly | missense_variant | 7/8 | 1 | NM_020358.2 | A2 | |
TRIM49 | ENST00000532501.2 | c.584C>G | p.Ala195Gly | missense_variant | 5/6 | 5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 139086Hom.: 0 Cov.: 21 FAILED QC
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GnomAD3 exomes AF: 0.0000872 AC: 9AN: 103250Hom.: 0 AF XY: 0.0000916 AC XY: 5AN XY: 54608
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000340 AC: 46AN: 1353444Hom.: 0 Cov.: 26 AF XY: 0.0000478 AC XY: 32AN XY: 669914
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GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 139086Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 67368
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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 | Jan 29, 2024 | The c.815C>G (p.A272G) alteration is located in exon 7 (coding exon 5) of the TRIM49 gene. This alteration results from a C to G substitution at nucleotide position 815, causing the alanine (A) at amino acid position 272 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
M;.
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Gain of disorder (P = 0.0359);.;
MVP
MPC
ClinPred
T
GERP RS
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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