chr15-76204109-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000388942.9(TMEM266):c.1366G>A(p.Ala456Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM266 | NM_152335.5 | c.1366G>A | p.Ala456Thr | missense_variant | 11/11 | ENST00000388942.9 | |
TMEM266 | XM_047432151.1 | c.1390G>A | p.Ala464Thr | missense_variant | 13/13 | ||
TMEM266 | XM_017021915.2 | c.1390G>A | p.Ala464Thr | missense_variant | 13/13 | ||
TMEM266 | XM_005254160.4 | c.838G>A | p.Ala280Thr | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM266 | ENST00000388942.9 | c.1366G>A | p.Ala456Thr | missense_variant | 11/11 | 5 | NM_152335.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000809 AC: 2AN: 247350Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134664
GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460602Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 726548
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.1390G>A (p.A464T) alteration is located in exon 11 (coding exon 10) of the TMEM266 gene. This alteration results from a G to A substitution at nucleotide position 1390, causing the alanine (A) at amino acid position 464 to be replaced by a threonine (T). 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