chrX-15845525-G-GA
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001272071.2(AP1S2):c.289-10_289-9insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000548 in 1,062,827 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 47 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., 12 hem., cov: 22)
Exomes 𝑓: 0.00058 ( 0 hom. 35 hem. )
Consequence
AP1S2
NM_001272071.2 splice_polypyrimidine_tract, intron
NM_001272071.2 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.89
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.
BP6
Variant X-15845525-G-GA is Benign according to our data. Variant chrX-15845525-G-GA is described in ClinVar as [Benign]. Clinvar id is 2039329.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAd4 at 12 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP1S2 | NM_001272071.2 | c.289-10_289-9insT | splice_polypyrimidine_tract_variant, intron_variant | ENST00000672987.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP1S2 | ENST00000672987.1 | c.289-10_289-9insT | splice_polypyrimidine_tract_variant, intron_variant | NM_001272071.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000241 AC: 24AN: 99649Hom.: 0 Cov.: 22 AF XY: 0.000442 AC XY: 12AN XY: 27123
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GnomAD3 exomes AF: 0.00129 AC: 145AN: 112281Hom.: 0 AF XY: 0.000218 AC XY: 8AN XY: 36773
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GnomAD4 exome AF: 0.000579 AC: 558AN: 963163Hom.: 0 Cov.: 32 AF XY: 0.000115 AC XY: 35AN XY: 303189
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GnomAD4 genome AF: 0.000241 AC: 24AN: 99664Hom.: 0 Cov.: 22 AF XY: 0.000442 AC XY: 12AN XY: 27156
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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 | Oct 24, 2023 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at