chr15-62692930-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015059.3(TLN2):āc.1204A>Gā(p.Ile402Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000546 in 1,612,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I402T) has been classified as Uncertain significance.
Frequency
Consequence
NM_015059.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLN2 | NM_015059.3 | c.1204A>G | p.Ile402Val | missense_variant | 13/59 | ENST00000636159.2 | |
TLN2 | NM_001394547.1 | c.1204A>G | p.Ile402Val | missense_variant | 12/58 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLN2 | ENST00000636159.2 | c.1204A>G | p.Ile402Val | missense_variant | 13/59 | 5 | NM_015059.3 | P1 | |
TLN2 | ENST00000561311.5 | c.1204A>G | p.Ile402Val | missense_variant | 12/58 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248924Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134540
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1459864Hom.: 0 Cov.: 30 AF XY: 0.0000496 AC XY: 36AN XY: 726162
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.1204A>G (p.I402V) alteration is located in exon 10 (coding exon 10) of the TLN2 gene. This alteration results from a A to G substitution at nucleotide position 1204, causing the isoleucine (I) at amino acid position 402 to be replaced by a valine (V). 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