7-100180880-GTTTTT-GTT
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_001282717.2(STAG3):c.116+223_116+225delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00247 in 221,350 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 0.0000073 ( 0 hom., cov: 27)
Exomes 𝑓: 0.0065 ( 0 hom. )
Consequence
STAG3
NM_001282717.2 intron
NM_001282717.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.666
Publications
0 publications found
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 8Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- spermatogenic failure 61Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
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
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| STAG3 | NM_001282717.2 | MANE Select | c.116+223_116+225delTTT | intron | N/A | NP_001269646.1 | D6W5U7 | ||
| STAG3 | NM_001375438.1 | c.116+223_116+225delTTT | intron | N/A | NP_001362367.1 | D6W5U7 | |||
| STAG3 | NM_001282716.1 | c.116+223_116+225delTTT | intron | N/A | NP_001269645.1 | Q9UJ98-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| STAG3 | ENST00000615138.5 | TSL:1 MANE Select | c.116+199_116+201delTTT | intron | N/A | ENSP00000477973.1 | D6W5U7 | ||
| STAG3 | ENST00000317296.9 | TSL:1 | c.116+199_116+201delTTT | intron | N/A | ENSP00000319318.5 | Q9UJ98-1 | ||
| STAG3 | ENST00000426455.5 | TSL:1 | c.116+199_116+201delTTT | intron | N/A | ENSP00000400359.1 | Q9UJ98-1 |
Frequencies
GnomAD3 genomes 0.00000731 AC: 1AN: 136828Hom.: 0 Cov.: 27 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
136828
Hom.:
Cov.:
27
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.00646 AC: 546AN: 84522Hom.: 0 AF XY: 0.00600 AC XY: 276AN XY: 46014 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
AF:
AC:
546
AN:
84522
Hom.:
AF XY:
AC XY:
276
AN XY:
46014
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
13
AN:
1952
American (AMR)
AF:
AC:
22
AN:
3108
Ashkenazi Jewish (ASJ)
AF:
AC:
15
AN:
2104
East Asian (EAS)
AF:
AC:
22
AN:
4888
South Asian (SAS)
AF:
AC:
95
AN:
11436
European-Finnish (FIN)
AF:
AC:
25
AN:
5176
Middle Eastern (MID)
AF:
AC:
2
AN:
272
European-Non Finnish (NFE)
AF:
AC:
318
AN:
50652
Other (OTH)
AF:
AC:
34
AN:
4934
⚠️ 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: 0.261
Heterozygous variant carriers
0
56
112
167
223
279
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
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>80
Age
GnomAD4 genome 0.00000731 AC: 1AN: 136828Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 65572 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
136828
Hom.:
Cov.:
27
AF XY:
AC XY:
0
AN XY:
65572
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
37392
American (AMR)
AF:
AC:
0
AN:
13448
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3286
East Asian (EAS)
AF:
AC:
0
AN:
4750
South Asian (SAS)
AF:
AC:
0
AN:
4300
European-Finnish (FIN)
AF:
AC:
0
AN:
7484
Middle Eastern (MID)
AF:
AC:
0
AN:
274
European-Non Finnish (NFE)
AF:
AC:
0
AN:
63182
Other (OTH)
AF:
AC:
0
AN:
1844
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 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: 0.275
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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