8-9556178-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003747.3(TNKS):c.239C>T(p.Ser80Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,612,648 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.239C>T | p.Ser80Phe | missense_variant | 1/27 | ENST00000310430.11 | NP_003738.2 | |
TNKS | XM_011543845.4 | c.239C>T | p.Ser80Phe | missense_variant | 1/28 | XP_011542147.1 | ||
TNKS | XM_011543846.4 | c.239C>T | p.Ser80Phe | missense_variant | 1/27 | XP_011542148.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNKS | ENST00000310430.11 | c.239C>T | p.Ser80Phe | missense_variant | 1/27 | 1 | NM_003747.3 | ENSP00000311579 | P1 | |
TNKS | ENST00000517770.2 | c.239C>T | p.Ser80Phe | missense_variant | 1/28 | 4 | ENSP00000428185 | |||
TNKS | ENST00000520408.5 | c.239C>T | p.Ser80Phe | missense_variant | 1/11 | 2 | ENSP00000428299 | |||
TNKS | ENST00000522110.1 | c.239C>T | p.Ser80Phe | missense_variant | 1/1 | ENSP00000430920 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152240Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000116 AC: 29AN: 249502Hom.: 0 AF XY: 0.000104 AC XY: 14AN XY: 135040
GnomAD4 exome AF: 0.000144 AC: 210AN: 1460408Hom.: 0 Cov.: 31 AF XY: 0.000127 AC XY: 92AN XY: 726286
GnomAD4 genome AF: 0.000118 AC: 18AN: 152240Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.239C>T (p.S80F) alteration is located in exon 1 (coding exon 1) of the TNKS gene. This alteration results from a C to T substitution at nucleotide position 239, causing the serine (S) at amino acid position 80 to be replaced by a phenylalanine (F). 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