10-91798715-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_025235.4(TNKS2):c.25G>A(p.Gly9Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000242 in 1,237,470 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_025235.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNKS2 | NM_025235.4 | c.25G>A | p.Gly9Arg | missense_variant | 1/27 | ENST00000371627.5 | |
TNKS2 | XM_011540213.2 | c.25G>A | p.Gly9Arg | missense_variant | 1/27 | ||
TNKS2 | XM_017016701.2 | c.25G>A | p.Gly9Arg | missense_variant | 1/13 | ||
TNKS2 | XM_047425795.1 | c.25G>A | p.Gly9Arg | missense_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNKS2 | ENST00000371627.5 | c.25G>A | p.Gly9Arg | missense_variant | 1/27 | 1 | NM_025235.4 | P1 | |
TNKS2 | ENST00000710380.1 | c.64G>A | p.Gly22Arg | missense_variant | 1/27 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151882Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000230 AC: 25AN: 1085588Hom.: 0 Cov.: 30 AF XY: 0.0000195 AC XY: 10AN XY: 513550
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151882Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.25G>A (p.G9R) alteration is located in exon 1 (coding exon 1) of the TNKS2 gene. This alteration results from a G to A substitution at nucleotide position 25, causing the glycine (G) at amino acid position 9 to be replaced by an arginine (R). 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