rs440666
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000484.4(APP):c.1459-106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,522,872 control chromosomes in the GnomAD database, including 407,666 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.71 ( 38203 hom., cov: 32)
Exomes 𝑓: 0.73 ( 369463 hom. )
Consequence
APP
NM_000484.4 intron
NM_000484.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.337
Genes affected
APP (HGNC:620): (amyloid beta precursor protein) This gene encodes a cell surface receptor and transmembrane precursor protein that is cleaved by secretases to form a number of peptides. Some of these peptides are secreted and can bind to the acetyltransferase complex APBB1/TIP60 to promote transcriptional activation, while others form the protein basis of the amyloid plaques found in the brains of patients with Alzheimer disease. In addition, two of the peptides are antimicrobial peptides, having been shown to have bacteriocidal and antifungal activities. Mutations in this gene have been implicated in autosomal dominant Alzheimer disease and cerebroarterial amyloidosis (cerebral amyloid angiopathy). Multiple transcript variants encoding several different isoforms have been found for this gene. [provided by RefSeq, Aug 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 21-25955861-T-C is Benign according to our data. Variant chr21-25955861-T-C is described in ClinVar as [Benign]. Clinvar id is 1250029.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APP | NM_000484.4 | c.1459-106A>G | intron_variant | ENST00000346798.8 | NP_000475.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APP | ENST00000346798.8 | c.1459-106A>G | intron_variant | 1 | NM_000484.4 | ENSP00000284981.4 |
Frequencies
GnomAD3 genomes AF: 0.706 AC: 107353AN: 151968Hom.: 38177 Cov.: 32
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GnomAD4 exome AF: 0.733 AC: 1005099AN: 1370786Hom.: 369463 AF XY: 0.735 AC XY: 505017AN XY: 686948
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GnomAD4 genome AF: 0.706 AC: 107423AN: 152086Hom.: 38203 Cov.: 32 AF XY: 0.705 AC XY: 52418AN XY: 74334
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at