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
Consequence
NM_001080495.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNRC18 | ENST00000430969.6 | c.8669G>A | p.Arg2890Gln | missense_variant | Exon 29 of 30 | 5 | NM_001080495.3 | ENSP00000395538.1 | ||
TNRC18 | ENST00000399537.8 | c.8669G>A | p.Arg2890Gln | missense_variant | Exon 29 of 30 | 5 | ENSP00000382452.4 |
Frequencies
GnomAD3 genomes AF: 0.0000527 AC: 8AN: 151830Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.000210 AC: 305AN: 1453556Hom.: 1 Cov.: 36 AF XY: 0.000212 AC XY: 153AN XY: 722440
GnomAD4 genome AF: 0.0000527 AC: 8AN: 151830Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74158
ClinVar
Submissions by phenotype
not specified Uncertain:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at