chr7-100181901-C-CAA

Position:

• chr7-100181901-C-CAA

Variant summary

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

The NM_001282717.2(STAG3):​c.117-172_117-171dupAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 69,916 control chromosomes in the GnomAD database, including 1,837 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (1837 hom., cov: 25)
• Consequence: STAG3 NM_001282717.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.471

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 7-100181901-C-CAA is Benign according to our data. Variant chr7-100181901-C-CAA is described in ClinVar as [Benign]. Clinvar id is 1254489.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAG3	NM_001282717.2	c.117-172_117-171dupAA		intron_variant		ENST00000615138.5	NP_001269646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAG3	ENST00000615138.5	c.117-189_117-188insAA		intron_variant		1	NM_001282717.2	ENSP00000477973.1

Frequencies

GnomAD3 genomes AF: 0.265 AC: 18520 AN: 69938 Hom.: 1837 Cov.: 25

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.265 AC: 18509 AN: 69916 Hom.: 1837 Cov.: 25 AF XY: 0.261 AC XY: 8482 AN XY: 32466

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.290

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

Jun 04, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3041317; hg19: chr7-99779524;