chrX-15845153-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001272071.2(AP1S2):c.426+226A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 751,502 control chromosomes in the GnomAD database, including 16,114 homozygotes. There are 55,479 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.24 ( 2360 hom., 7905 hem., cov: 22)
Exomes 𝑓: 0.25 ( 13754 hom. 47574 hem. )
Consequence
AP1S2
NM_001272071.2 intron
NM_001272071.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.562
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 Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant X-15845153-T-C is Benign according to our data. Variant chrX-15845153-T-C is described in ClinVar as [Benign]. Clinvar id is 1264730.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP1S2 | NM_001272071.2 | c.426+226A>G | intron_variant | ENST00000672987.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP1S2 | ENST00000672987.1 | c.426+226A>G | intron_variant | NM_001272071.2 | P3 |
Frequencies
GnomAD3 genomes AF: 0.242 AC: 26829AN: 111032Hom.: 2362 Cov.: 22 AF XY: 0.237 AC XY: 7892AN XY: 33238
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GnomAD4 exome AF: 0.247 AC: 158488AN: 640418Hom.: 13754 Cov.: 24 AF XY: 0.248 AC XY: 47574AN XY: 192074
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GnomAD4 genome AF: 0.242 AC: 26846AN: 111084Hom.: 2360 Cov.: 22 AF XY: 0.237 AC XY: 7905AN XY: 33300
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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