Genetic Variant NM_152524.6:c.26G>A (chr2-200533001-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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. 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.

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

Publications

21 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SGO2	NM_152524.6 link	c.26G>A	p.Gly9Asp	missense_variant	Exon 2 of 9	ENST00000357799.9	NP_689737.4	Q562F6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SGO2	ENST00000357799.9 link	c.26G>A	p.Gly9Asp	missense_variant	Exon 2 of 9	1	NM_152524.6	ENSP00000350447.4	Q562F6-1
SGO2	ENST00000409203.3 link	c.26G>A	p.Gly9Asp	missense_variant	Exon 2 of 6	1		ENSP00000386249.3	Q562F6-3
SGO2	ENST00000418045.5 link	c.26G>A	p.Gly9Asp	missense_variant	Exon 3 of 4	5		ENSP00000393325.1	C9JW92
SGO2	ENST00000460534.1 link	n.155G>A		non_coding_transcript_exon_variant	Exon 2 of 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

GnomAD2 exomes

AF:

0.0884

AC:

21719

AN:

245606

AF XY:

0.0871

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 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

African (AFR)

AF:

0.0105

AC:

349

AN:

33252

American (AMR)

AF:

0.145

AC:

6366

AN:

43936

Ashkenazi Jewish (ASJ)

AF:

0.0616

AC:

1601

AN:

26006

East Asian (EAS)

AF:

0.0819

AC:

3239

AN:

39554

South Asian (SAS)

AF:

0.0743

AC:

6315

AN:

84952

European-Finnish (FIN)

AF:

0.152

AC:

8108

AN:

53366

Middle Eastern (MID)

AF:

0.0434

AC:

245

AN:

5650

European-Non Finnish (NFE)

AF:

0.0737

AC:

81814

AN:

1110494

Other (OTH)

AF:

0.0710

AC:

4278

AN:

60228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

4817

9634

14450

19267

24084

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3006

6012

9018

12024

15030

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0680

AC:

10318

AN:

151746

Hom.:

509

Cov.:

AF XY:

0.0713

AC XY:

5282

AN XY:

74112

show subpopulations

African (AFR)

AF:

0.0154

AC:

636

AN:

41386

American (AMR)

AF:

0.0965

AC:

1472

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.0600

AC:

208

AN:

3466

East Asian (EAS)

AF:

0.0833

AC:

431

AN:

5174

South Asian (SAS)

AF:

0.0665

AC:

319

AN:

4794

European-Finnish (FIN)

AF:

0.155

AC:

1616

AN:

10444

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0789

AC:

5357

AN:

67920

Other (OTH)

AF:

0.0597

AC:

126

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

455

909

1364

1818

2273

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

118

236

354

472

590

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0719

Hom.:

1167

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

(source)

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

PhyloP100

0.21

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

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over