rs139972151

Positions:

• chr1-226883771-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4 BS1_Supporting BS2

The NM_000447.3(PSEN2):​c.208G>A​(p.Gly70Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,614,072 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000059 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000046 (0 hom.)
• Consequence: PSEN2 NM_000447.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4 B:1
• Conservation: PhyloP100: 3.07

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 Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.40273646).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0000458 (67/1461866) while in subpopulation NFE AF= 0.0000567 (63/1112008). AF 95% confidence interval is 0.0000452. There are 0 homozygotes in gnomad4_exome. There are 32 alleles in male gnomad4_exome subpopulation. Median coverage is 43. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High AC in GnomAd4 at 9 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PSEN2	NM_000447.3	c.208G>A	p.Gly70Arg	missense_variant	5/13	ENST00000366783.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PSEN2	ENST00000366783.8	c.208G>A	p.Gly70Arg	missense_variant	5/13	5	NM_000447.3	P4

Frequencies

GnomAD3 genomes AF: 0.0000591 AC: 9 AN: 152206 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000483

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000882

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000637 AC: 16 AN: 251294 Hom.: 0 AF XY: 0.0000736 AC XY: 10 AN XY: 135858

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000578

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000114

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000458 AC: 67 AN: 1461866 Hom.: 0 Cov.: 43 AF XY: 0.0000440 AC XY: 32 AN XY: 727222

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000447

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000232

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000567

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000591 AC: 9 AN: 152206 Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6 AN XY: 74362

Gnomad4 AFR AF: 0.0000483

Gnomad4 AMR AF: 0.0000654

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000882

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000116 Hom.: 0

Bravo AF: 0.0000718

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.0000576 AC: 7

EpiCase AF: 0.000109

EpiControl AF: 0.000356

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:4 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:2 Benign:1

Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The PSEN2 p.Gly70Arg variant was identified in 1 of 454 proband chromosomes (frequency: 0.0022) from a cohort of 227 unrelated probands clinically diagnosed for Alzheimer disease with symptoms occuring before 70 years old (Wojtas_2012_PMID:23383383). The variant was identified in dbSNP (ID: rs139972151) and ClinVar (classified as likely benign by Biesecker Lab). The variant was identified in control databases in 17 of 282688 chromosomes at a frequency of 0.00006014 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 14 of 129028 chromosomes (freq: 0.000109), Latino in 2 of 35436 chromosomes (freq: 0.000056) and South Asian in 1 of 30616 chromosomes (freq: 0.000033), but was not observed in the African, Ashkenazi Jewish, East Asian, European (Finnish), or Other populations. The p.Gly70 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Oct 29, 2021	The PSEN2 c.208G>A; p.Gly70Arg variant (rs139972151) has been described in at least two individuals who had a clinical diagnosis of Alzheimer’s disease, but no additional clinical information was available (Wojtas 2012, see link to Alzheimer’s Association International Conference (AAIC) 2019 abstract). This variant contains an entry in ClinVar (Variation ID: 192129), and is found in the non-Finnish European population with an allele frequency of 0.011% (14/129028 alleles) in the Genome Aggregation Database. The glycine at codon 70 is weakly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.456). However, given the lack of clinical and functional data, the significance of the p.Gly70Arg variant is uncertain at this time. REFERENCES Wojtas A et al. C9ORF72 repeat expansions and other FTD gene mutations in a clinical AD patient series from Mayo Clinic. Am J Neurodegener Dis. 2012;1(1):107-18. PMID: 23383383. Link to AAIC 2019 P3-120 abstract: https://alz-journals.onlinelibrary.wiley.com/doi/full/10.1016/j.jalz.2019.06.3148 -
Likely benign, criteria provided, single submitter	research	Biesecker Lab/Clinical Genomics Section, National Institutes of Health	Jun 24, 2013	- -

PSEN2-related disorder Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 26, 2023

The PSEN2 c.208G>A variant is predicted to result in the amino acid substitution p.Gly70Arg. This variant was reported in a patient with early-onset Alzheimer's disease (Wojtas et al. 2012. PubMed ID: 23383383) and as a likely benign variant in a study of patients with coronary artery disease risk (Ng et al. 2013. PubMed ID: 23861362). It is reported in 0.011% of alleles in individuals of European (Non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Alzheimer disease 4 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Mar 26, 2021

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individual(s) with Alzheimer disease (PMID: 23383383). ClinVar contains an entry for this variant (Variation ID: 192129). This variant is present in population databases (rs139972151, ExAC 0.009%). This sequence change replaces glycine with arginine at codon 70 of the PSEN2 protein (p.Gly70Arg). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and arginine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.046	T
BayesDel_noAF	Benign	-0.10
CADD	Benign	20
DANN	Uncertain	1.0
DEOGEN2	Benign	0.26	T;.;.;.;.
Eigen	Benign	-0.22
Eigen_PC	Benign	-0.078
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Uncertain	0.89	D;D;D;.;D
M_CAP	Uncertain	0.22	D
MetaRNN	Benign	0.40	T;T;T;T;T
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Benign	0.90	L;.;L;.;.
MutationTaster	Benign	0.99	D;D;D;D;D
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	-0.33	N;N;N;N;.
REVEL	Uncertain	0.46
Sift	Benign	0.12	T;T;T;T;.
Sift4G	Benign	0.28	T;T;T;T;T
Polyphen		0.010	B;.;.;.;.
Vest4		0.43
MutPred		0.26		Gain of solvent accessibility (P = 0.0037);Gain of solvent accessibility (P = 0.0037);Gain of solvent accessibility (P = 0.0037);.;.;
MVP		0.97
MPC		0.31
ClinPred		0.080	T
GERP RS		4.4
Varity_R		0.061
gMVP		0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs139972151; hg19: chr1-227071472; COSMIC: COSV60919106; COSMIC: COSV60919106;