Variant chr7-100180396-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001282717.2(STAG3):c.-64-97G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 601,726 control chromosomes in the GnomAD database, including 27,845 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 7293 hom., cov: 31)

Exomes 𝑓: 0.28 ( 20552 hom. )

Consequence

STAG3
NM_001282717.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.546

Variant links:

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]

STAG3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 7-100180396-G-C is Benign according to our data. Variant chr7-100180396-G-C is described in ClinVar as [Benign]. Clinvar id is 1267511.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	Protein	UniProt
STAG3	NM_001282717.2 link	c.-64-97G>C		intron_variant		ENST00000615138.5	NP_001269646.1	Q9UJ98D6W5U7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAG3	ENST00000615138.5 link	c.-64-97G>C		intron_variant		1	NM_001282717.2	ENSP00000477973.1		D6W5U7

Frequencies

GnomAD3 genomes

AF:

0.293

AC:

44541

AN:

151810

Hom.:

7274

Cov.:

show subpopulations

Gnomad AFR

AF:

0.318

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.428

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.625

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.266

GnomAD4 exome

AF:

0.279

AC:

125524

AN:

449796

Hom.:

20552

AF XY:

0.273

AC XY:

65886

AN XY:

240972

show subpopulations

Gnomad4 AFR exome

AF:

0.312

Gnomad4 AMR exome

AF:

0.505

Gnomad4 ASJ exome

AF:

0.187

Gnomad4 EAS exome

AF:

0.604

Gnomad4 SAS exome

AF:

0.244

Gnomad4 FIN exome

AF:

0.255

Gnomad4 NFE exome

AF:

0.238

Gnomad4 OTH exome

AF:

0.258

GnomAD4 genome

AF:

0.294

AC:

44596

AN:

151930

Hom.:

7293

Cov.:

AF XY:

0.298

AC XY:

22137

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.318

Gnomad4 AMR

AF:

0.429

Gnomad4 ASJ

AF:

0.177

Gnomad4 EAS

AF:

0.625

Gnomad4 SAS

AF:

0.265

Gnomad4 FIN

AF:

0.258

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.259

Hom.:

683

Bravo

AF:

0.310

Asia WGS

AF:

0.429

AC:

1494

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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

-0.89

CADD

Benign

0.92

DANN

Benign

0.61

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over