Genetic Variant STAG3:c.116+222_116+225delTTTT (chr7-100180880-GTTTT-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001282717.2(STAG3):c.116+222_116+225delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00151 in 84,830 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 27)

Exomes 𝑓: 0.0015 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

STAG3
NM_001282717.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.901

Publications

0 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)
spermatogenic failure 61
Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

STAG3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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.116+222_116+225delTTTT	intron	N/A	NP_001269646.1	D6W5U7
STAG3	NM_001375438.1		c.116+222_116+225delTTTT	intron	N/A	NP_001362367.1	D6W5U7
STAG3	NM_001282716.1		c.116+222_116+225delTTTT	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.116+207_116+210delTTTT	intron	N/A	ENSP00000477973.1	D6W5U7
STAG3	ENST00000317296.9	TSL:1	c.116+207_116+210delTTTT	intron	N/A	ENSP00000319318.5	Q9UJ98-1
STAG3	ENST00000426455.5	TSL:1	c.116+207_116+210delTTTT	intron	N/A	ENSP00000400359.1	Q9UJ98-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

136838

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00151

AC:

128

AN:

84830

Hom.:

AF XY:

0.00139

AC XY:

AN XY:

46178

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00102

AC:

AN:

1956

American (AMR)

AF:

0.00192

AC:

AN:

3118

Ashkenazi Jewish (ASJ)

AF:

0.00237

AC:

AN:

2106

East Asian (EAS)

AF:

0.00204

AC:

AN:

4902

South Asian (SAS)

AF:

0.00192

AC:

AN:

11478

European-Finnish (FIN)

AF:

0.00115

AC:

AN:

5204

Middle Eastern (MID)

AF:

0.00

AC:

AN:

276

European-Non Finnish (NFE)

AF:

0.00140

AC:

AN:

50824

Other (OTH)

AF:

0.00121

AC:

AN:

4966

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.245

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

136838

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

65574

African (AFR)

AF:

0.00

AC:

AN:

37392

American (AMR)

AF:

0.00

AC:

AN:

13450

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3286

East Asian (EAS)

AF:

0.00

AC:

AN:

4750

South Asian (SAS)

AF:

0.00

AC:

AN:

4300

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7488

Middle Eastern (MID)

AF:

0.00

AC:

AN:

274

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

63186

Other (OTH)

AF:

0.00

AC:

AN:

1844

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.90

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

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7-100180880-GTTTTT-GT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over