7-5308906-C-T

Variant summary

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

The NM_001080495.3(TNRC18):​c.8669G>A​(p.Arg2890Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000195 in 1,605,386 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00021 ( 1 hom. )

Consequence

TNRC18
NM_001080495.3 missense

Scores

2
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.52
Variant links:
Genes affected
TNRC18 (HGNC:11962): (trinucleotide repeat containing 18) Predicted to enable chromatin binding activity. Located in cytosol; mitochondrion; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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=0.04566428).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TNRC18NM_001080495.3 linkc.8669G>A p.Arg2890Gln missense_variant Exon 29 of 30 ENST00000430969.6 NP_001073964.2 O15417-1A3KMH2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TNRC18ENST00000430969.6 linkc.8669G>A p.Arg2890Gln missense_variant Exon 29 of 30 5 NM_001080495.3 ENSP00000395538.1 O15417-1
TNRC18ENST00000399537.8 linkc.8669G>A p.Arg2890Gln missense_variant Exon 29 of 30 5 ENSP00000382452.4 H9KVB4

Frequencies

GnomAD3 genomes
AF:
0.0000527
AC:
8
AN:
151830
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000210
AC:
305
AN:
1453556
Hom.:
1
Cov.:
36
AF XY:
0.000212
AC XY:
153
AN XY:
722440
show subpopulations
Gnomad4 AFR exome
AF:
0.0000602
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.0000354
Gnomad4 FIN exome
AF:
0.0000190
Gnomad4 NFE exome
AF:
0.000255
Gnomad4 OTH exome
AF:
0.000234
GnomAD4 genome
AF:
0.0000527
AC:
8
AN:
151830
Hom.:
0
Cov.:
32
AF XY:
0.0000270
AC XY:
2
AN XY:
74158
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000158
Hom.:
0
Bravo
AF:
0.0000831
ExAC
AF:
0.000382
AC:
46

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Mar 02, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.8669G>A (p.R2890Q) alteration is located in exon 29 (coding exon 28) of the TNRC18 gene. This alteration results from a G to A substitution at nucleotide position 8669, causing the arginine (R) at amino acid position 2890 to be replaced by a glutamine (Q). 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
0.065
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.66
CADD
Benign
19
DANN
Uncertain
0.98
DEOGEN2
Benign
0.25
T;T
Eigen
Benign
-0.59
Eigen_PC
Benign
-0.34
FATHMM_MKL
Benign
0.45
N
LIST_S2
Benign
0.83
T;T
M_CAP
Uncertain
0.15
D
MetaRNN
Benign
0.046
T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
-0.81
.;N
PrimateAI
Benign
0.32
T
PROVEAN
Benign
-0.56
N;N
REVEL
Benign
0.071
Sift
Benign
0.63
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.010
.;B
Vest4
0.25
MutPred
0.22
Loss of MoRF binding (P = 0.014);Loss of MoRF binding (P = 0.014);
MVP
0.043
MPC
0.62
ClinPred
0.094
T
GERP RS
2.8
Varity_R
0.043
gMVP
0.22

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: rs750268247; hg19: chr7-5348537; API