chr3-195867383-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001382273.1(TNK2):c.2915G>A(p.Arg972Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000517 in 1,604,232 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R972W) has been classified as Uncertain significance.
Frequency
Consequence
NM_001382273.1 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 |
---|---|---|---|---|---|---|---|
TNK2 | NM_001382273.1 | c.2915G>A | p.Arg972Gln | missense_variant | 13/16 | ENST00000672887.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNK2 | ENST00000672887.2 | c.2915G>A | p.Arg972Gln | missense_variant | 13/16 | NM_001382273.1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000676 AC: 15AN: 221874Hom.: 0 AF XY: 0.0000327 AC XY: 4AN XY: 122234
GnomAD4 exome AF: 0.0000503 AC: 73AN: 1451892Hom.: 1 Cov.: 38 AF XY: 0.0000429 AC XY: 31AN XY: 722048
GnomAD4 genome ? AF: 0.0000656 AC: 10AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.3104G>A (p.R1035Q) alteration is located in exon 13 (coding exon 13) of the TNK2 gene. This alteration results from a G to A substitution at nucleotide position 3104, causing the arginine (R) at amino acid position 1035 to be replaced by a glutamine (Q). 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