X-124022370-CA-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001042750.2(STAG2):c.-97-145del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.90 (25602 hom., 13132 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: STAG2 NM_001042750.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0160

Genes affected

STAG2 (HGNC:11355): (STAG2 cohesin complex component) The protein encoded by this gene is a subunit of the cohesin complex, which regulates the separation of sister chromatids during cell division. Targeted inactivation of this gene results in chromatid cohesion defects and aneuploidy, suggesting that genetic disruption of cohesin is a cause of aneuploidy in human cancer. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant X-124022370-CA-C is Benign according to our data. Variant chrX-124022370-CA-C is described in ClinVar as [Benign]. Clinvar id is 1243394.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAG2	NM_001042750.2	c.-97-145del		intron_variant		ENST00000371145.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAG2	ENST00000371145.8	c.-97-145del		intron_variant		1	NM_001042750.2	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 70519 AN: 77972 Hom.: 25620 Cov.: 0 AF XY: 0.948 AC XY: 13133 AN XY: 13848 FAILED QC

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.965

Gnomad EAS AF: 0.950

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.950

Gnomad NFE AF: 0.970

Gnomad OTH AF: 0.906

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.904 AC: 70480 AN: 77934 Hom.: 25602 Cov.: 0 AF XY: 0.948 AC XY: 13132 AN XY: 13848

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.965

Gnomad4 EAS AF: 0.950

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.895

Gnomad4 NFE AF: 0.970

Gnomad4 OTH AF: 0.906

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

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: rs5903652; hg19: chrX-123156220;