17-78049495-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142640.2(TNRC6C):c.1063A>T(p.Thr355Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,614,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142640.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNRC6C | NM_001142640.2 | c.1063A>T | p.Thr355Ser | missense_variant | 5/23 | ENST00000696270.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6C | ENST00000696270.1 | c.1063A>T | p.Thr355Ser | missense_variant | 5/23 | NM_001142640.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249168Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135162
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461706Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727132
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152368Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 19, 2023 | The c.433A>T (p.T145S) alteration is located in exon 4 (coding exon 1) of the TNRC6C gene. This alteration results from a A to T substitution at nucleotide position 433, causing the threonine (T) at amino acid position 145 to be replaced by a serine (S). 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