chr15-45682565-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_021199.4(SQOR):c.952G>A(p.Val318Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00255 in 1,614,220 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_021199.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SQOR | NM_021199.4 | c.952G>A | p.Val318Met | missense_variant | Exon 7 of 10 | ENST00000260324.12 | NP_067022.1 | |
SQOR | NM_001271213.2 | c.952G>A | p.Val318Met | missense_variant | Exon 8 of 11 | NP_001258142.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SQOR | ENST00000260324.12 | c.952G>A | p.Val318Met | missense_variant | Exon 7 of 10 | 1 | NM_021199.4 | ENSP00000260324.7 | ||
SQOR | ENST00000568606.5 | c.952G>A | p.Val318Met | missense_variant | Exon 8 of 11 | 5 | ENSP00000456019.1 | |||
SQOR | ENST00000565997.1 | c.25G>A | p.Val9Met | missense_variant | Exon 1 of 3 | 2 | ENSP00000454953.1 |
Frequencies
GnomAD3 genomes AF: 0.00162 AC: 247AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00190 AC: 478AN: 251416Hom.: 0 AF XY: 0.00202 AC XY: 274AN XY: 135888
GnomAD4 exome AF: 0.00265 AC: 3876AN: 1461884Hom.: 6 Cov.: 31 AF XY: 0.00262 AC XY: 1902AN XY: 727244
GnomAD4 genome AF: 0.00162 AC: 247AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.00153 AC XY: 114AN XY: 74482
ClinVar
Submissions by phenotype
SQOR-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at