NM_017439.4:c.577-12_577-11dupTT
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_017439.4(GSAP):c.577-12_577-11dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.013 ( 27 hom., cov: 0)
Exomes 𝑓: 0.0044 ( 2 hom. )
Consequence
GSAP
NM_017439.4 intron
NM_017439.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00
Genes affected
GSAP (HGNC:28042): (gamma-secretase activating protein) Accumulation of neurotoxic amyloid-beta is a major hallmark of Alzheimer disease (AD; MIM 104300). Formation of amyloid-beta is catalyzed by gamma-secretase (see PSEN1; MIM 104311), a protease with numerous substrates. PION, or GSAP, selectively increases amyloid-beta production through a mechanism involving its interaction with both gamma-secretase and its substrate, the amyloid-beta precursor protein (APP; MIM 104760) C-terminal fragment (APP-CTF) (He et al., 2010 [PubMed 20811458]).[supplied by OMIM, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0132 (1295/98022) while in subpopulation AMR AF= 0.0383 (316/8246). AF 95% confidence interval is 0.0348. There are 27 homozygotes in gnomad4. There are 629 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 27 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0132 AC: 1297AN: 98020Hom.: 27 Cov.: 0
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GnomAD4 exome AF: 0.00437 AC: 4731AN: 1082486Hom.: 2 Cov.: 0 AF XY: 0.00429 AC XY: 2284AN XY: 532692
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GnomAD4 genome AF: 0.0132 AC: 1295AN: 98022Hom.: 27 Cov.: 0 AF XY: 0.0139 AC XY: 629AN XY: 45102
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at