7-5308110-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001080495.3(TNRC18):c.8903G>A(p.Cys2968Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000165 in 1,397,520 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.000016 ( 0 hom. )
Consequence
TNRC18
NM_001080495.3 missense
NM_001080495.3 missense
Scores
7
7
4
Clinical Significance
Conservation
PhyloP100: 7.24
Genes affected
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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 |
---|---|---|---|---|---|---|---|
TNRC18 | NM_001080495.3 | c.8903G>A | p.Cys2968Tyr | missense_variant | 30/30 | ENST00000430969.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC18 | ENST00000430969.6 | c.8903G>A | p.Cys2968Tyr | missense_variant | 30/30 | 5 | NM_001080495.3 | P4 | |
TNRC18 | ENST00000399537.8 | c.8903G>A | p.Cys2968Tyr | missense_variant | 30/30 | 5 | A2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156854Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83234
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GnomAD4 exome AF: 0.0000165 AC: 23AN: 1397520Hom.: 0 Cov.: 30 AF XY: 0.0000116 AC XY: 8AN XY: 689336
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GnomAD4 genome Cov.: 34
GnomAD4 genome
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34
Bravo
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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 | Sep 29, 2023 | The c.8903G>A (p.C2968Y) alteration is located in exon 30 (coding exon 29) of the TNRC18 gene. This alteration results from a G to A substitution at nucleotide position 8903, causing the cysteine (C) at amino acid position 2968 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Pathogenic
D;D
Polyphen
1.0
.;D
Vest4
MutPred
Gain of solvent accessibility (P = 0.0018);Gain of solvent accessibility (P = 0.0018);
MVP
MPC
0.91
ClinPred
D
GERP RS
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