7-100180880-G-GT

Variant names:

• chr7-100180880-G-GT
• rs35965210
• NM_001282717.2:c.116+225dupT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001282717.2(STAG3):​c.116+225dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 221,346 control chromosomes in the GnomAD database, including 2,137 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.16 (2126 hom., cov: 27)
  • Exomes 𝑓: 0.26 (11 hom.)
• Consequence: STAG3 NM_001282717.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0530

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 Benign. Variant got -10 ACMG points.

• BP6: Variant 7-100180880-G-GT is Benign according to our data. Variant chr7-100180880-G-GT is described in ClinVar as [Benign]. Clinvar id is 1269361.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAG3	NM_001282717.2	c.116+225dupT		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.116+201_116+202insT		intron_variant	Intron 2 of 33	1	NM_001282717.2	ENSP00000477973.1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 21541 AN: 136750 Hom.: 2126 Cov.: 27

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.0613

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.256 AC: 21686 AN: 84594 Hom.: 11 Cov.: 0 AF XY: 0.259 AC XY: 11923 AN XY: 46020

Gnomad4 AFR exome AF: 0.241

Gnomad4 AMR exome AF: 0.252

Gnomad4 ASJ exome AF: 0.284

Gnomad4 EAS exome AF: 0.237

Gnomad4 SAS exome AF: 0.264

Gnomad4 FIN exome AF: 0.260

Gnomad4 NFE exome AF: 0.257

Gnomad4 OTH exome AF: 0.247

GnomAD4 genome AF: 0.157 AC: 21531 AN: 136752 Hom.: 2126 Cov.: 27 AF XY: 0.155 AC XY: 10153 AN XY: 65560

Gnomad4 AFR AF: 0.0648

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.358

Gnomad4 EAS AF: 0.0615

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.185

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 24, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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: rs35965210; hg19: chr7-99778503;