15-62819540-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015059.3(TLN2):āc.6796T>Gā(p.Phe2266Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F2266L) has been classified as Likely benign.
Frequency
Consequence
NM_015059.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TLN2 | ENST00000636159.2 | c.6796T>G | p.Phe2266Val | missense_variant | 53/59 | 5 | NM_015059.3 | ENSP00000490662.2 | ||
TLN2 | ENST00000489129.5 | n.4711T>G | non_coding_transcript_exon_variant | 21/27 | 1 | |||||
TLN2 | ENST00000561311.5 | c.6796T>G | p.Phe2266Val | missense_variant | 52/58 | 5 | ENSP00000453508.1 | |||
TLN2 | ENST00000494733.5 | c.3538T>G | p.Phe1180Val | missense_variant | 26/32 | 5 | ENSP00000453730.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251090Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135710
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461780Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727194
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152202Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74418
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at