21-25901777-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000484.4(APP):c.1963+3247A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 152,016 control chromosomes in the GnomAD database, including 58,473 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (58473 hom., cov: 30)
• Consequence: APP NM_000484.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APP	NM_000484.4	c.1963+3247A>C		intron_variant		ENST00000346798.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APP	ENST00000346798.8	c.1963+3247A>C		intron_variant		1	NM_000484.4

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133061 AN: 151898 Hom.: 58435 Cov.: 30

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.907

Gnomad OTH AF: 0.875

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.876 AC: 133153 AN: 152016 Hom.: 58473 Cov.: 30 AF XY: 0.874 AC XY: 64901 AN XY: 74288

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.895

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.884

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.907

Gnomad4 OTH AF: 0.875

Alfa AF: 0.900 Hom.: 84422

Bravo AF: 0.875

Asia WGS AF: 0.868 AC: 3020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1787438; hg19: chr21-27274089;