chr2-223765159-CCATCAT-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001039569.2(AP1S3):c.429+48_429+53delATGATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000389 in 1,560,500 control chromosomes in the GnomAD database, including 5 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00028 ( 1 hom., cov: 0)
Exomes 𝑓: 0.00040 ( 4 hom. )
Consequence
AP1S3
NM_001039569.2 intron
NM_001039569.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.815
Genes affected
AP1S3 (HGNC:18971): (adaptor related protein complex 1 subunit sigma 3) This gene encodes a member of the adaptor-related protein complex 1, sigma subunit genes. The encoded protein is a component of adaptor protein complex 1 (AP-1), one of the AP complexes involved in claathrin-mediated vesicular transport from the Golgi or endosomes. Disruption of the pathway for display of HIV-1 antigens, which prevents recognition of the virus by cytotoxic T cells, has been shown to involve the AP-1 complex (PMID: 15569716). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 42 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AP1S3 | NM_001039569.2 | c.429+48_429+53delATGATG | intron_variant | Intron 4 of 4 | ENST00000396654.7 | NP_001034658.1 | ||
AP1S3 | XM_011510600.4 | c.292-6415_292-6410delATGATG | intron_variant | Intron 3 of 3 | XP_011508902.1 | |||
AP1S3 | NR_110905.2 | n.600+48_600+53delATGATG | intron_variant | Intron 5 of 5 | ||||
AP1S3 | NR_110906.2 | n.452+48_452+53delATGATG | intron_variant | Intron 3 of 3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AP1S3 | ENST00000396654.7 | c.429+48_429+53delATGATG | intron_variant | Intron 4 of 4 | 2 | NM_001039569.2 | ENSP00000379891.2 | |||
ENSG00000286239 | ENST00000650969.1 | n.*1393+48_*1393+53delATGATG | intron_variant | Intron 16 of 16 | ENSP00000498456.1 |
Frequencies
GnomAD3 genomes AF: 0.000278 AC: 42AN: 150904Hom.: 1 Cov.: 0
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GnomAD3 exomes AF: 0.000396 AC: 80AN: 201824Hom.: 0 AF XY: 0.000391 AC XY: 43AN XY: 109964
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GnomAD4 exome AF: 0.000401 AC: 565AN: 1409476Hom.: 4 AF XY: 0.000408 AC XY: 286AN XY: 700752
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GnomAD4 genome AF: 0.000278 AC: 42AN: 151024Hom.: 1 Cov.: 0 AF XY: 0.000203 AC XY: 15AN XY: 73738
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at