7-100181901-C-A

Variant names:

• chr7-100181901-C-A
• rs1370780612
• NM_001282717.2:c.117-189C>A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_001282717.2(STAG3):​c.117-189C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.041 (0 hom., cov: 12)
  • Failed GnomAD Quality Control
• Consequence: STAG3 NM_001282717.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.643

Genes affected

STAG3 (HGNC:11356): (STAG3 cohesin complex component) The protein encoded by this gene is expressed in the nucleus and is a subunit of the cohesin complex which regulates the cohesion of sister chromatids during cell division. A mutation in this gene is associated with premature ovarian failure. Alternate splicing results in multiple transcript variants encoding distinct isoforms. This gene has multiple pseudogenes. [provided by RefSeq, Apr 2014]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 7-100181901-C-A is Benign according to our data. Variant chr7-100181901-C-A is described in ClinVar as [Benign]. Clinvar id is 1236920.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAG3	NM_001282717.2	c.117-189C>A		intron_variant	Intron 2 of 33	ENST00000615138.5	NP_001269646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAG3	ENST00000615138.5	c.117-189C>A		intron_variant	Intron 2 of 33	1	NM_001282717.2	ENSP00000477973.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2771 AN: 67420 Hom.: 0 Cov.: 12 FAILED QC

Gnomad AFR AF: 0.0623

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.0187

Gnomad NFE AF: 0.0335

Gnomad OTH AF: 0.0333

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: AS_VQSR AF: 0.0410 AC: 2766 AN: 67400 Hom.: 0 Cov.: 12 AF XY: 0.0411 AC XY: 1290 AN XY: 31424

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.0414

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.0627

Gnomad4 SAS AF: 0.0423

Gnomad4 FIN AF: 0.0404

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.0342

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 03, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.0
DANN	Benign	0.81

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: rs1370780612; hg19: chr7-99779524;