17-78049144-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142640.2(TNRC6C):c.712G>A(p.Val238Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000292 in 1,608,110 control chromosomes in the GnomAD database, including 1 homozygotes. 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.712G>A | p.Val238Ile | missense_variant | 5/23 | ENST00000696270.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNRC6C | ENST00000696270.1 | c.712G>A | p.Val238Ile | missense_variant | 5/23 | NM_001142640.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000287 AC: 7AN: 243894Hom.: 1 AF XY: 0.0000378 AC XY: 5AN XY: 132232
GnomAD4 exome AF: 0.0000282 AC: 41AN: 1455898Hom.: 1 Cov.: 32 AF XY: 0.0000332 AC XY: 24AN XY: 723900
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 04, 2024 | The c.82G>A (p.V28I) alteration is located in exon 4 (coding exon 1) of the TNRC6C gene. This alteration results from a G to A substitution at nucleotide position 82, causing the valine (V) at amino acid position 28 to be replaced by an isoleucine (I). 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