3-136338358-T-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 2P and 14B. PM2BP4_StrongBP6_ModerateBS1BS2
The ENST00000383202.7(STAG1):c.3753+12A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,456,490 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
STAG1
ENST00000383202.7 intron
ENST00000383202.7 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.191
Genes affected
STAG1 (HGNC:11354): (STAG1 cohesin complex component) This gene is a member of the SCC3 family and is expressed in the nucleus. It encodes a component of cohesin, a multisubunit protein complex that provides sister chromatid cohesion along the length of a chromosome from DNA replication through prophase and prometaphase, after which it is dissociated in preparation for segregation during anaphase. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 3-136338358-T-C is Benign according to our data. Variant chr3-136338358-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2025430.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00000343 (5/1456490) while in subpopulation AMR AF= 0.0000895 (4/44696). AF 95% confidence interval is 0.0000299. There are 0 homozygotes in gnomad4_exome. There are 1 alleles in male gnomad4_exome subpopulation. Median coverage is 28. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STAG1 | NM_005862.3 | c.3753+12A>G | intron_variant | ENST00000383202.7 | NP_005853.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STAG1 | ENST00000383202.7 | c.3753+12A>G | intron_variant | 1 | NM_005862.3 | ENSP00000372689 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250746Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135598
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GnomAD4 exome AF: 0.00000343 AC: 5AN: 1456490Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1AN XY: 724972
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GnomAD4 genome Cov.: 33
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33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 04, 2023 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at