chr15-76204014-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000388942.9(TMEM266):c.1271A>C(p.Gln424Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 1,608,886 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.1271A>C | p.Gln424Pro | missense_variant | 11/11 | ENST00000388942.9 | |
TMEM266 | XM_047432151.1 | c.1295A>C | p.Gln432Pro | missense_variant | 13/13 | ||
TMEM266 | XM_017021915.2 | c.1295A>C | p.Gln432Pro | missense_variant | 13/13 | ||
TMEM266 | XM_005254160.4 | c.743A>C | p.Gln248Pro | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM266 | ENST00000388942.9 | c.1271A>C | p.Gln424Pro | missense_variant | 11/11 | 5 | NM_152335.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151992Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000244 AC: 6AN: 246084Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 133932
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1456894Hom.: 0 Cov.: 32 AF XY: 0.00000414 AC XY: 3AN XY: 723810
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151992Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.1295A>C (p.Q432P) alteration is located in exon 11 (coding exon 10) of the TMEM266 gene. This alteration results from a A to C substitution at nucleotide position 1295, causing the glutamine (Q) at amino acid position 432 to be replaced by a proline (P). 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