7-100182263-G-A

Position:

• chr7-100182263-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001282717.2(STAG3):​c.219+71G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 1,154,580 control chromosomes in the GnomAD database, including 53,202 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.31 (7910 hom., cov: 29)
  • Exomes 𝑓: 0.29 (45292 hom.)
• Consequence: STAG3 NM_001282717.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 7-100182263-G-A is Benign according to our data. Variant chr7-100182263-G-A is described in ClinVar as [Benign]. Clinvar id is 1239681.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAG3	NM_001282717.2	c.219+71G>A		intron_variant		ENST00000615138.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAG3	ENST00000615138.5	c.219+71G>A		intron_variant		1	NM_001282717.2	A2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46745 AN: 151428 Hom.: 7891 Cov.: 29

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.283

GnomAD4 exome AF: 0.286 AC: 286402 AN: 1003034 Hom.: 45292 AF XY: 0.282 AC XY: 144412 AN XY: 512606

Gnomad4 AFR exome AF: 0.316

Gnomad4 AMR exome AF: 0.539

Gnomad4 ASJ exome AF: 0.189

Gnomad4 EAS exome AF: 0.606

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.275

Gnomad4 NFE exome AF: 0.265

Gnomad4 OTH exome AF: 0.275

GnomAD4 genome AF: 0.309 AC: 46799 AN: 151546 Hom.: 7910 Cov.: 29 AF XY: 0.312 AC XY: 23121 AN XY: 74016

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.284

Alfa AF: 0.277 Hom.: 783

Bravo AF: 0.325

Asia WGS AF: 0.432 AC: 1504 AN: 3478

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 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.1
DANN	Benign	0.86

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: rs6465764; hg19: chr7-99779886; COSMIC: COSV52785005; COSMIC: COSV52785005;