chrX-15845830-A-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001272071.2(AP1S2):c.288+73T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 1.0 ( 38564 hom., 32602 hem., cov: 22)
Exomes 𝑓: 0.99 ( 285810 hom. 239252 hem. )
Failed GnomAD Quality Control
Consequence
AP1S2
NM_001272071.2 intron
NM_001272071.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.132
Genes affected
AP1S2 (HGNC:560): (adaptor related protein complex 1 subunit sigma 2) Adaptor protein complex 1 is found at the cytoplasmic face of coated vesicles located at the Golgi complex, where it mediates both the recruitment of clathrin to the membrane and the recognition of sorting signals within the cytosolic tails of transmembrane receptors. This complex is a heterotetramer composed of two large, one medium, and one small adaptin subunit. The protein encoded by this gene serves as the small subunit of this complex and is a member of the adaptin protein family. Transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BP6
Variant X-15845830-A-T is Benign according to our data. Variant chrX-15845830-A-T is described in ClinVar as [Benign]. Clinvar id is 1276725.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP1S2 | NM_001272071.2 | c.288+73T>A | intron_variant | ENST00000672987.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP1S2 | ENST00000672987.1 | c.288+73T>A | intron_variant | NM_001272071.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 110037AN: 110518Hom.: 38568 Cov.: 22 AF XY: 0.996 AC XY: 32545AN XY: 32662 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.993 AC: 814890AN: 820361Hom.: 285810 AF XY: 0.994 AC XY: 239252AN XY: 240667
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.996 AC: 110085AN: 110566Hom.: 38564 Cov.: 22 AF XY: 0.996 AC XY: 32602AN XY: 32720
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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 | GeneDx | May 10, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at