chr2-200571273-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152524.6(SGO2):c.927T>A(p.Asn309Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152524.6 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 |
---|---|---|---|---|---|---|---|
SGO2 | NM_152524.6 | c.927T>A | p.Asn309Lys | missense_variant | 7/9 | ENST00000357799.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGO2 | ENST00000357799.9 | c.927T>A | p.Asn309Lys | missense_variant | 7/9 | 1 | NM_152524.6 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000444 AC: 11AN: 247838Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134452
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461138Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726826
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.927T>A (p.N309K) alteration is located in exon 7 (coding exon 6) of the SGO2 gene. This alteration results from a T to A substitution at nucleotide position 927, causing the asparagine (N) at amino acid position 309 to be replaced by a lysine (K). 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