8-9556386-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003747.3(TNKS):āc.447C>Gā(p.Ser149Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,614,114 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_003747.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNKS | NM_003747.3 | c.447C>G | p.Ser149Arg | missense_variant | 1/27 | ENST00000310430.11 | NP_003738.2 | |
TNKS | XM_011543845.4 | c.447C>G | p.Ser149Arg | missense_variant | 1/28 | XP_011542147.1 | ||
TNKS | XM_011543846.4 | c.447C>G | p.Ser149Arg | missense_variant | 1/27 | XP_011542148.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNKS | ENST00000310430.11 | c.447C>G | p.Ser149Arg | missense_variant | 1/27 | 1 | NM_003747.3 | ENSP00000311579 | P1 | |
TNKS | ENST00000517770.2 | c.447C>G | p.Ser149Arg | missense_variant | 1/28 | 4 | ENSP00000428185 | |||
TNKS | ENST00000520408.5 | c.447C>G | p.Ser149Arg | missense_variant | 1/11 | 2 | ENSP00000428299 | |||
TNKS | ENST00000522110.1 | c.447C>G | p.Ser149Arg | missense_variant | 1/1 | ENSP00000430920 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251452Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135920
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.447C>G (p.S149R) alteration is located in exon 1 (coding exon 1) of the TNKS gene. This alteration results from a C to G substitution at nucleotide position 447, causing the serine (S) at amino acid position 149 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