chr2-200533001-G-C

Variant names:

• chr2-200533001-G-C
• NM_152524.6:c.26G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_152524.6(SGO2):​c.26G>C​(p.Gly9Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G9D) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SGO2 NM_152524.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

SGO2 (HGNC:30812): (shugoshin 2) Predicted to be involved in homologous chromosome segregation; meiotic sister chromatid cohesion; and mitotic sister chromatid segregation. Predicted to act upstream of or within meiotic nuclear division; positive regulation of maintenance of meiotic sister chromatid cohesion, centromeric; and protein localization. Located in chromosome, centromeric region and nuclear body. Part of mitotic cohesin complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.049595863).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGO2	NM_152524.6	c.26G>C	p.Gly9Ala	missense_variant	Exon 2 of 9	ENST00000357799.9	NP_689737.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGO2	ENST00000357799.9	c.26G>C	p.Gly9Ala	missense_variant	Exon 2 of 9	1	NM_152524.6	ENSP00000350447.4
SGO2	ENST00000409203.3	c.26G>C	p.Gly9Ala	missense_variant	Exon 2 of 6	1		ENSP00000386249.3
SGO2	ENST00000418045.5	c.26G>C	p.Gly9Ala	missense_variant	Exon 3 of 4	5		ENSP00000393325.1
SGO2	ENST00000460534.1	n.155G>C		non_coding_transcript_exon_variant	Exon 2 of 2	4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.55
CADD	Benign	12
DANN	Benign	0.86
DEOGEN2	Benign	0.056	.;T;.
Eigen	Benign	-0.74
Eigen_PC	Benign	-0.72
FATHMM_MKL	Benign	0.011	N
LIST_S2	Benign	0.75	T;T;T
M_CAP	Benign	0.0056	T
MetaRNN	Benign	0.050	T;T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.28	T
PROVEAN	Benign	-1.3	N;N;N
REVEL	Benign	0.11
Sift	Benign	0.28	T;D;T
Sift4G	Benign	0.70	T;T;T
Polyphen		0.11, 0.010	.;B;B
Vest4		0.088, 0.11
MutPred		0.22		Gain of sheet (P = 0.0344);Gain of sheet (P = 0.0344);Gain of sheet (P = 0.0344);
MVP		0.14
MPC		0.084
ClinPred		0.053	T
GERP RS		1.3
Varity_R		0.034
gMVP		0.023

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-201397724;