chr17-15636083-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001348119.1(TRIM16):c.802G>A(p.Glu268Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,609,598 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000040 ( 0 hom., cov: 28)
Exomes 𝑓: 0.000025 ( 4 hom. )
Consequence
TRIM16
NM_001348119.1 missense
NM_001348119.1 missense
Scores
2
12
Clinical Significance
Conservation
PhyloP100: 2.15
Genes affected
TRIM16 (HGNC:17241): (tripartite motif containing 16) The protein encoded by this gene is a tripartite motif (TRIM) family member that contains two B box domains and a coiled-coiled region that are characteristic of the B box zinc finger protein family. While it lacks a RING domain found in other TRIM proteins, the encoded protein can homodimerize or heterodimerize with other TRIM proteins and has E3 ubiquitin ligase activity. This gene is also a tumor suppressor and is involved in secretory autophagy. [provided by RefSeq, Jan 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.02443704).
BS2
?
High Homozygotes in GnomAdExome at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIM16 | NM_001348119.1 | c.802G>A | p.Glu268Lys | missense_variant | 9/12 | ENST00000649191.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM16 | ENST00000649191.2 | c.802G>A | p.Glu268Lys | missense_variant | 9/12 | NM_001348119.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000398 AC: 6AN: 150736Hom.: 0 Cov.: 28
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000144 AC: 36AN: 250468Hom.: 4 AF XY: 0.000133 AC XY: 18AN XY: 135370
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GnomAD4 exome AF: 0.0000254 AC: 37AN: 1458752Hom.: 4 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 725624
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GnomAD4 genome ? AF: 0.0000398 AC: 6AN: 150846Hom.: 0 Cov.: 28 AF XY: 0.0000543 AC XY: 4AN XY: 73668
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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 | Mar 22, 2023 | The c.802G>A (p.E268K) alteration is located in exon 6 (coding exon 3) of the TRIM16 gene. This alteration results from a G to A substitution at nucleotide position 802, causing the glutamic acid (E) at amino acid position 268 to be replaced by a lysine (K). 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
Uncertain
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T;.;T;T;.;D;D;T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Benign
T
Sift4G
Benign
T;T;T;T;T;T;.;D;.;T;T
Polyphen
0.21, 0.35
.;.;B;B;.;B;B;.;.;.;.
Vest4
MVP
MPC
0.32
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
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