2-200539971-C-T

Variant summary

Our verdict is Benign. Variant got -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

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 Benign. Variant got -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/exons	MANE	UniProt
SGO2	NM_152524.6	c.388-2608C>T		intron_variant		ENST00000357799.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGO2	ENST00000357799.9	c.388-2608C>T		intron_variant		1	NM_152524.6	P3
SGO2	ENST00000409203.3	c.388-2608C>T		intron_variant		1		A2
SGO2	ENST00000469840.1	n.110-2608C>T		intron_variant, non_coding_transcript_variant		3
SGO2	ENST00000488636.5	n.205-2608C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.478

Alfa AF: 0.470 Hom.: 22440

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs842938; hg19: chr2-201404694;