chr15-76204216-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000388942.9(TMEM266):c.1473G>T(p.Arg491Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,206 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000388942.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM266 | NM_152335.5 | c.1473G>T | p.Arg491Ser | missense_variant | 11/11 | ENST00000388942.9 | |
TMEM266 | XM_047432151.1 | c.1497G>T | p.Arg499Ser | missense_variant | 13/13 | ||
TMEM266 | XM_017021915.2 | c.1497G>T | p.Arg499Ser | missense_variant | 13/13 | ||
TMEM266 | XM_005254160.4 | c.945G>T | p.Arg315Ser | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM266 | ENST00000388942.9 | c.1473G>T | p.Arg491Ser | missense_variant | 11/11 | 5 | NM_152335.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.1497G>T (p.R499S) alteration is located in exon 11 (coding exon 10) of the TMEM266 gene. This alteration results from a G to T substitution at nucleotide position 1497, causing the arginine (R) at amino acid position 499 to be replaced by a serine (S). 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