rs362356

chr14-73171921-G-C

Variant summary

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

The NM_000021.4(PSEN1):c.338+874G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.056 in 152,164 control chromosomes in the GnomAD database, including 326 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 0.056 (326 hom., cov: 32)
• Consequence: PSEN1 NM_000021.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

PSEN1 (HGNC:9508): (presenilin 1) Alzheimer's disease (AD) patients with an inherited form of the disease carry mutations in the presenilin proteins (PSEN1; PSEN2) or in the amyloid precursor protein (APP). These disease-linked mutations result in increased production of the longer form of amyloid-beta (main component of amyloid deposits found in AD brains). Presenilins are postulated to regulate APP processing through their effects on gamma-secretase, an enzyme that cleaves APP. Also, it is thought that the presenilins are involved in the cleavage of the Notch receptor, such that they either directly regulate gamma-secretase activity or themselves are protease enzymes. Several alternatively spliced transcript variants encoding different isoforms have been identified for this gene, the full-length nature of only some have been determined. [provided by RefSeq, Aug 2008]

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 = 0.0868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSEN1	NM_000021.4	c.338+874G>C		intron_variant		ENST00000324501.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSEN1	ENST00000324501.10	c.338+874G>C		intron_variant		1	NM_000021.4	P4

Frequencies

GnomAD3 genomes AF: 0.0561 AC: 8529 AN: 152046 Hom.: 326 Cov.: 32

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0417

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.00866

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0687

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0886

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0560 AC: 8528 AN: 152164 Hom.: 326 Cov.: 32 AF XY: 0.0533 AC XY: 3965 AN XY: 74392

Gnomad4 AFR AF: 0.0161

Gnomad4 AMR AF: 0.0416

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.00868

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0687

Gnomad4 NFE AF: 0.0886

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0713 Hom.: 41

Bravo AF: 0.0533

Asia WGS AF: 0.0160 AC: 57 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	0.47
Dann	Benign	0.37

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: rs362356; hg19: chr14-73638629;