3-195866951-G-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001382273.1(TNK2):c.3099C>A(p.Phe1033Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000126 in 1,613,000 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 Likely benign (★).
Frequency
Consequence
NM_001382273.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNK2 | NM_001382273.1 | c.3099C>A | p.Phe1033Leu | missense_variant | 15/16 | ENST00000672887.2 | NP_001369202.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNK2 | ENST00000672887.2 | c.3099C>A | p.Phe1033Leu | missense_variant | 15/16 | NM_001382273.1 | ENSP00000499899.1 |
Frequencies
GnomAD3 genomes AF: 0.000716 AC: 109AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000157 AC: 39AN: 248868Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135062
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1460690Hom.: 0 Cov.: 34 AF XY: 0.0000495 AC XY: 36AN XY: 726694
GnomAD4 genome AF: 0.000709 AC: 108AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.000752 AC XY: 56AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at