1-226895849-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000447.3(PSEN2):c.*270C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 529,464 control chromosomes in the GnomAD database, including 69,053 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.49 (18641 hom., cov: 31)
  • Exomes 𝑓: 0.51 (50412 hom.)
• Consequence: PSEN2 NM_000447.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.655

Genes affected

PSEN2 (HGNC:9509): (presenilin 2) Alzheimer's disease (AD) patients with an inherited form of the disease carry mutations in the presenilin proteins (PSEN1 or PSEN2) or 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 act are protease enzymes. Two alternatively spliced transcript variants encoding different isoforms of PSEN2 have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 1-226895849-C-T is Benign according to our data. Variant chr1-226895849-C-T is described in ClinVar as [Benign]. Clinvar id is 296001.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSEN2	NM_000447.3	c.*270C>T		3_prime_UTR_variant	13/13	ENST00000366783.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSEN2	ENST00000366783.8	c.*270C>T		3_prime_UTR_variant	13/13	5	NM_000447.3	P4

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74472 AN: 151672 Hom.: 18629 Cov.: 31

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.527

GnomAD4 exome AF: 0.513 AC: 193691 AN: 377674 Hom.: 50412 Cov.: 3 AF XY: 0.508 AC XY: 101507 AN XY: 199766

Gnomad4 AFR exome AF: 0.407

Gnomad4 AMR exome AF: 0.523

Gnomad4 ASJ exome AF: 0.621

Gnomad4 EAS exome AF: 0.449

Gnomad4 SAS exome AF: 0.420

Gnomad4 FIN exome AF: 0.529

Gnomad4 NFE exome AF: 0.532

Gnomad4 OTH exome AF: 0.526

GnomAD4 genome AF: 0.491 AC: 74514 AN: 151790 Hom.: 18641 Cov.: 31 AF XY: 0.491 AC XY: 36447 AN XY: 74174

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.522

Alfa AF: 0.504 Hom.: 5975

Bravo AF: 0.489

Asia WGS AF: 0.419 AC: 1461 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Dilated cardiomyopathy 1V Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Alzheimer disease 4 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.80

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: rs8383; hg19: chr1-227083550; COSMIC: COSV60918495; COSMIC: COSV60918495;