chr2-200539971-C-T

Variant names:

• chr2-200539971-C-T
• rs842938
• NM_152524.6:c.388-2608C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152524.6(SGO2):​c.388-2608C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 150,742 control chromosomes in the GnomAD database, including 16,916 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (16916 hom., cov: 29)
• Consequence: SGO2 NM_152524.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGO2	NM_152524.6	c.388-2608C>T		intron_variant	Intron 4 of 8	ENST00000357799.9	NP_689737.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGO2	ENST00000357799.9	c.388-2608C>T		intron_variant	Intron 4 of 8	1	NM_152524.6	ENSP00000350447.4
SGO2	ENST00000409203.3	c.388-2608C>T		intron_variant	Intron 4 of 5	1		ENSP00000386249.3
SGO2	ENST00000469840.1	n.110-2608C>T		intron_variant	Intron 2 of 3	3
SGO2	ENST00000488636.5	n.205-2608C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71504 AN: 150624 Hom.: 16895 Cov.: 29

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.475

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.475 AC: 71565 AN: 150742 Hom.: 16916 Cov.: 29 AF XY: 0.477 AC XY: 35102 AN XY: 73650

African (AFR) AF: 0.463 AC: 19002 AN: 41048

American (AMR) AF: 0.504 AC: 7638 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1754 AN: 3448

East Asian (EAS) AF: 0.485 AC: 2485 AN: 5126

South Asian (SAS) AF: 0.531 AC: 2494 AN: 4700

European-Finnish (FIN) AF: 0.462 AC: 4833 AN: 10470

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31707 AN: 67498

Other (OTH) AF: 0.478 AC: 1001 AN: 2096

Alfa AF: 0.471 Hom.: 26617

Bravo AF: 0.474

Asia WGS AF: 0.497 AC: 1727 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.26
DANN	Benign	0.51
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs842938; hg19: chr2-201404694;