12-64414979-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007235.6(XPOT):āc.133A>Gā(p.Arg45Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,610,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007235.6 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 |
---|---|---|---|---|---|---|---|
XPOT | NM_007235.6 | c.133A>G | p.Arg45Gly | missense_variant | 3/25 | ENST00000332707.10 | |
XPOT | XM_017018748.2 | c.133A>G | p.Arg45Gly | missense_variant | 3/25 | ||
XPOT | XM_047428193.1 | c.133A>G | p.Arg45Gly | missense_variant | 3/25 | ||
XPOT | XM_047428194.1 | c.133A>G | p.Arg45Gly | missense_variant | 3/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPOT | ENST00000332707.10 | c.133A>G | p.Arg45Gly | missense_variant | 3/25 | 2 | NM_007235.6 | P1 | |
XPOT | ENST00000400935.2 | c.133A>G | p.Arg45Gly | missense_variant | 2/6 | 2 | |||
XPOT | ENST00000540203.5 | c.133A>G | p.Arg45Gly | missense_variant | 3/4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 250862Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135656
GnomAD4 exome AF: 0.0000206 AC: 30AN: 1457968Hom.: 0 Cov.: 29 AF XY: 0.0000289 AC XY: 21AN XY: 725574
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152332Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74498
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at