Variant 2-200533001-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152524.6(SGO2):c.26G>A(p.Gly9Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0762 in 1,609,184 control chromosomes in the GnomAD database, including 5,517 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.068 ( 509 hom., cov: 32)

Exomes 𝑓: 0.077 ( 5008 hom. )

Consequence

SGO2
NM_152524.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.211

Variant links:

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]

SGO2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013193488).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGO2	NM_152524.6 linkuse as main transcript	c.26G>A	p.Gly9Asp	missense_variant	2/9	ENST00000357799.9	NP_689737.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGO2	ENST00000357799.9 linkuse as main transcript	c.26G>A	p.Gly9Asp	missense_variant	2/9	1	NM_152524.6	ENSP00000350447	P3	Q562F6-1
SGO2	ENST00000409203.3 linkuse as main transcript	c.26G>A	p.Gly9Asp	missense_variant	2/6	1		ENSP00000386249	A2	Q562F6-3
SGO2	ENST00000418045.5 linkuse as main transcript	c.26G>A	p.Gly9Asp	missense_variant	3/4	5		ENSP00000393325
SGO2	ENST00000460534.1 linkuse as main transcript	n.155G>A		non_coding_transcript_exon_variant	2/2	4

Frequencies

GnomAD3 genomes

AF:

0.0680

AC:

10312

AN:

151628

Hom.:

507

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0154

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.0966

Gnomad ASJ

AF:

0.0600

Gnomad EAS

AF:

0.0831

Gnomad SAS

AF:

0.0661

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0788

Gnomad OTH

AF:

0.0599

GnomAD3 exomes

AF:

0.0884

AC:

21719

AN:

245606

Hom.:

1201

AF XY:

0.0871

AC XY:

11599

AN XY:

133110

show subpopulations

Gnomad AFR exome

AF:

0.0119

Gnomad AMR exome

AF:

0.152

Gnomad ASJ exome

AF:

0.0609

Gnomad EAS exome

AF:

0.0872

Gnomad SAS exome

AF:

0.0694

Gnomad FIN exome

AF:

0.149

Gnomad NFE exome

AF:

0.0764

Gnomad OTH exome

AF:

0.0762

GnomAD4 exome

AF:

0.0771

AC:

112315

AN:

1457438

Hom.:

5008

Cov.:

AF XY:

0.0777

AC XY:

56294

AN XY:

724774

show subpopulations

Gnomad4 AFR exome

AF:

0.0105

Gnomad4 AMR exome

AF:

0.145

Gnomad4 ASJ exome

AF:

0.0616

Gnomad4 EAS exome

AF:

0.0819

Gnomad4 SAS exome

AF:

0.0743

Gnomad4 FIN exome

AF:

0.152

Gnomad4 NFE exome

AF:

0.0737

Gnomad4 OTH exome

AF:

0.0710

GnomAD4 genome

AF:

0.0680

AC:

10318

AN:

151746

Hom.:

509

Cov.:

AF XY:

0.0713

AC XY:

5282

AN XY:

74112

show subpopulations

Gnomad4 AFR

AF:

0.0154

Gnomad4 AMR

AF:

0.0965

Gnomad4 ASJ

AF:

0.0600

Gnomad4 EAS

AF:

0.0833

Gnomad4 SAS

AF:

0.0665

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.0789

Gnomad4 OTH

AF:

0.0597

Alfa

AF:

0.0742

Hom.:

994

Bravo

AF:

0.0620

TwinsUK

AF:

0.0655

AC:

243

ALSPAC

AF:

0.0776

AC:

299

ESP6500AA

AF:

0.0139

AC:

ESP6500EA

AF:

0.0696

AC:

566

ExAC

AF:

0.0846

AC:

10221

Asia WGS

AF:

0.0760

AC:

264

AN:

3470

EpiCase

AF:

0.0720

EpiControl

AF:

0.0689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.66

DEOGEN2

Benign

0.053

.;T;.

Eigen

Benign

-0.82

Eigen_PC

Benign

-0.77

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.60

T;T;T

MetaRNN

Benign

0.0013

T;T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.30

PROVEAN

Benign

-1.3

N;N;N

REVEL

Benign

0.086

Sift

Benign

0.96

T;T;T

Sift4G

Benign

0.56

T;T;T

Polyphen

0.0040, 0.0010

.;B;B

Vest4

0.031, 0.018

MPC

0.080

ClinPred

0.00059

GERP RS

1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.029

gMVP

0.019

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over