dbSNP rs3041317: STAG3:c.117-179_117-171delAAAAAAAAA (chr7-100181901-CAAAAAAAAA-C) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001282717.2(STAG3):c.117-179_117-171delAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 25)

Consequence

STAG3
NM_001282717.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.792

Publications

1 publications found

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 Gene-Disease associations (from GenCC):

premature ovarian failure 8
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia
spermatogenic failure 61
Inheritance: AR Classification: STRONG, LIMITED Submitted by: PanelApp Australia, Labcorp Genetics (formerly Invitae)

STAG3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282717.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STAG3	NM_001282717.2	MANE Select	c.117-179_117-171delAAAAAAAAA	intron	N/A	NP_001269646.1	D6W5U7
STAG3	NM_001375438.1		c.117-179_117-171delAAAAAAAAA	intron	N/A	NP_001362367.1	D6W5U7
STAG3	NM_001282716.1		c.117-179_117-171delAAAAAAAAA	intron	N/A	NP_001269645.1	Q9UJ98-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
STAG3	ENST00000615138.5	TSL:1 MANE Select	c.117-188_117-180delAAAAAAAAA	intron	N/A	ENSP00000477973.1	D6W5U7
STAG3	ENST00000317296.9	TSL:1	c.117-188_117-180delAAAAAAAAA	intron	N/A	ENSP00000319318.5	Q9UJ98-1
STAG3	ENST00000426455.5	TSL:1	c.117-188_117-180delAAAAAAAAA	intron	N/A	ENSP00000400359.1	Q9UJ98-1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.79

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over