chrX-124025922-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001042750.2(STAG2):c.123+4T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,141,301 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 81 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., 9 hem., cov: 21)
Exomes 𝑓: 0.00024 ( 0 hom. 72 hem. )
Consequence
STAG2
NM_001042750.2 splice_donor_region, intron
NM_001042750.2 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.003827
2
Clinical Significance
Conservation
PhyloP100: 0.938
Genes affected
STAG2 (HGNC:11355): (STAG2 cohesin complex component) The protein encoded by this gene is a subunit of the cohesin complex, which regulates the separation of sister chromatids during cell division. Targeted inactivation of this gene results in chromatid cohesion defects and aneuploidy, suggesting that genetic disruption of cohesin is a cause of aneuploidy in human cancer. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant X-124025922-T-C is Benign according to our data. Variant chrX-124025922-T-C is described in ClinVar as [Benign]. Clinvar id is 1164890.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd at 9 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAG2 | NM_001042750.2 | c.123+4T>C | splice_donor_region_variant, intron_variant | ENST00000371145.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAG2 | ENST00000371145.8 | c.123+4T>C | splice_donor_region_variant, intron_variant | 1 | NM_001042750.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000182 AC: 20AN: 110054Hom.: 0 Cov.: 21 AF XY: 0.000278 AC XY: 9AN XY: 32326
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GnomAD3 exomes AF: 0.000114 AC: 19AN: 166706Hom.: 0 AF XY: 0.000128 AC XY: 7AN XY: 54714
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GnomAD4 exome AF: 0.000240 AC: 247AN: 1031247Hom.: 0 Cov.: 20 AF XY: 0.000235 AC XY: 72AN XY: 306409
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 06, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at