chrX-15827389-TGA-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001272071.2(AP1S2):c.436-19_436-18del variant causes a intron change. The variant allele was found at a frequency of 0.00000252 in 1,188,921 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000089 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.0000019 ( 0 hom. 1 hem. )
Consequence
AP1S2
NM_001272071.2 intron
NM_001272071.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.56
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]
ZRSR2 (HGNC:23019): (zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2) This gene encodes an essential splicing factor. The encoded protein associates with the U2 auxiliary factor heterodimer, which is required for the recognition of a functional 3' splice site in pre-mRNA splicing, and may play a role in network interactions during spliceosome assembly. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant X-15827389-TGA-T is Benign according to our data. Variant chrX-15827389-TGA-T is described in ClinVar as [Likely_benign]. Clinvar id is 1636652.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.436-19_436-18del | intron_variant | ENST00000672987.1 | |||
AP1S2 | NM_003916.5 | c.427-19_427-18del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP1S2 | ENST00000672987.1 | c.436-19_436-18del | intron_variant | NM_001272071.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000893 AC: 1AN: 112038Hom.: 0 Cov.: 22 AF XY: 0.0000292 AC XY: 1AN XY: 34206
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GnomAD3 exomes AF: 0.00000549 AC: 1AN: 182027Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 67005
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GnomAD4 exome AF: 0.00000186 AC: 2AN: 1076883Hom.: 0 AF XY: 0.00000290 AC XY: 1AN XY: 344857
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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 | Invitae | Mar 15, 2021 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at