7-5308170-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001080495.3(TNRC18):​c.8843C>T​(p.Ala2948Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000022 in 1,589,140 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000022 ( 0 hom. )

Consequence

TNRC18
NM_001080495.3 missense

Scores

10
8
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.31
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 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 rank MANE Protein UniProt
TNRC18NM_001080495.3 linkc.8843C>T p.Ala2948Val missense_variant Exon 30 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.8843C>T p.Ala2948Val missense_variant Exon 30 of 30 5 NM_001080495.3 ENSP00000395538.1 O15417-1
TNRC18ENST00000399537.8 linkc.8843C>T p.Ala2948Val missense_variant Exon 30 of 30 5 ENSP00000382452.4 H9KVB4

Frequencies

GnomAD3 genomes
AF:
0.0000197
AC:
3
AN:
152216
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
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:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000375
AC:
8
AN:
213432
Hom.:
0
AF XY:
0.0000517
AC XY:
6
AN XY:
115944
show subpopulations
Gnomad AFR exome
AF:
0.0000824
Gnomad AMR exome
AF:
0.0000989
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000375
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000317
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000223
AC:
32
AN:
1436924
Hom.:
0
Cov.:
34
AF XY:
0.0000238
AC XY:
17
AN XY:
712874
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000488
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000242
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000236
Gnomad4 OTH exome
AF:
0.0000337
GnomAD4 genome
AF:
0.0000197
AC:
3
AN:
152216
Hom.:
0
Cov.:
33
AF XY:
0.0000269
AC XY:
2
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000264
ExAC
AF:
0.0000497
AC:
6

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Oct 11, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.8843C>T (p.A2948V) alteration is located in exon 30 (coding exon 29) of the TNRC18 gene. This alteration results from a C to T substitution at nucleotide position 8843, causing the alanine (A) at amino acid position 2948 to be replaced by a valine (V). 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
Pathogenic
0.58
BayesDel_addAF
Pathogenic
0.16
D
BayesDel_noAF
Pathogenic
0.20
CADD
Pathogenic
31
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.60
D;T
Eigen
Pathogenic
0.77
Eigen_PC
Pathogenic
0.72
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Uncertain
0.97
D;D
M_CAP
Pathogenic
0.50
D
MetaRNN
Uncertain
0.55
D;D
MetaSVM
Uncertain
0.62
D
MutationAssessor
Uncertain
2.7
.;M
PrimateAI
Pathogenic
0.82
D
PROVEAN
Uncertain
-3.6
D;D
REVEL
Pathogenic
0.79
Sift
Uncertain
0.0010
D;D
Sift4G
Pathogenic
0.0
D;D
Polyphen
1.0
.;D
Vest4
0.59
MVP
0.33
MPC
0.53
ClinPred
0.32
T
GERP RS
4.5
Varity_R
0.47
gMVP
0.74

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: rs746930389; hg19: chr7-5347801; API