Genetic Variant NM_000447.3:c.69T>C (chr1-226881976-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_000447.3(PSEN2):c.69T>C(p.Ala23Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 1,613,976 control chromosomes in the GnomAD database, including 479,454 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.77 ( 45659 hom., cov: 33)

Exomes 𝑓: 0.77 ( 433795 hom. )

Consequence

PSEN2
NM_000447.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:15

Conservation

PhyloP100: -2.55

Publications

30 publications found

Variant links:

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]

PSEN2 Gene-Disease associations (from GenCC):

Alzheimer disease 4
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
early-onset autosomal dominant Alzheimer disease
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
familial isolated dilated cardiomyopathy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
dilated cardiomyopathy
Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

PSEN2 links:

ENSG00000288674 (HGNC:):

ENSG00000288674 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 1-226881976-T-C is Benign according to our data. Variant chr1-226881976-T-C is described in ClinVar as Benign. ClinVar VariationId is 256184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.55 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000447.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PSEN2	NM_000447.3	MANE Select	c.69T>C	p.Ala23Ala	synonymous	Exon 4 of 13	NP_000438.2	P49810-1
PSEN2	NM_001437537.1		c.69T>C	p.Ala23Ala	synonymous	Exon 3 of 12	NP_001424466.1
PSEN2	NM_012486.3		c.69T>C	p.Ala23Ala	synonymous	Exon 4 of 13	NP_036618.2	P49810-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PSEN2	ENST00000366783.8	TSL:5 MANE Select	c.69T>C	p.Ala23Ala	synonymous	Exon 4 of 13	ENSP00000355747.3	P49810-1
PSEN2	ENST00000366782.6	TSL:1	c.69T>C	p.Ala23Ala	synonymous	Exon 4 of 13	ENSP00000355746.2	P49810-1
ENSG00000288674	ENST00000366779.6	TSL:2	n.69T>C		non_coding_transcript_exon	Exon 4 of 32	ENSP00000355741.2

Frequencies

GnomAD3 genomes

AF:

0.773

AC:

117509

AN:

152036

Hom.:

45619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.816

Gnomad AMI

AF:

0.746

Gnomad AMR

AF:

0.732

Gnomad ASJ

AF:

0.766

Gnomad EAS

AF:

0.571

Gnomad SAS

AF:

0.744

Gnomad FIN

AF:

0.789

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.756

GnomAD2 exomes

AF:

0.756

AC:

190017

AN:

251334

AF XY:

0.758

show subpopulations

Gnomad AFR exome

AF:

0.816

Gnomad AMR exome

AF:

0.741

Gnomad ASJ exome

AF:

0.757

Gnomad EAS exome

AF:

0.554

Gnomad FIN exome

AF:

0.786

Gnomad NFE exome

AF:

0.778

Gnomad OTH exome

AF:

0.778

GnomAD4 exome

AF:

0.769

AC:

1124751

AN:

1461822

Hom.:

433795

Cov.:

AF XY:

0.769

AC XY:

559370

AN XY:

727212

show subpopulations

African (AFR)

AF:

0.827

AC:

27673

AN:

33478

American (AMR)

AF:

0.745

AC:

33307

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.766

AC:

20009

AN:

26134

East Asian (EAS)

AF:

0.628

AC:

24931

AN:

39698

South Asian (SAS)

AF:

0.754

AC:

65077

AN:

86258

European-Finnish (FIN)

AF:

0.785

AC:

41882

AN:

53382

Middle Eastern (MID)

AF:

0.822

AC:

4739

AN:

5768

European-Non Finnish (NFE)

AF:

0.774

AC:

860936

AN:

1111990

Other (OTH)

AF:

0.765

AC:

46197

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

16627

33254

49880

66507

83134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20520

41040

61560

82080

102600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.773

AC:

117600

AN:

152154

Hom.:

45659

Cov.:

AF XY:

0.772

AC XY:

57415

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.816

AC:

33897

AN:

41524

American (AMR)

AF:

0.732

AC:

11199

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.766

AC:

2658

AN:

3468

East Asian (EAS)

AF:

0.571

AC:

2944

AN:

5160

South Asian (SAS)

AF:

0.744

AC:

3588

AN:

4820

European-Finnish (FIN)

AF:

0.789

AC:

8363

AN:

10598

Middle Eastern (MID)

AF:

0.786

AC:

231

AN:

294

European-Non Finnish (NFE)

AF:

0.772

AC:

52447

AN:

67974

Other (OTH)

AF:

0.756

AC:

1593

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1367

2734

4101

5468

6835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

866

1732

2598

3464

4330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.773

Hom.:

193054

Bravo

AF:

0.773

Asia WGS

AF:

0.690

AC:

2400

AN:

3478

EpiCase

AF:

0.771

EpiControl

AF:

0.779

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (7)

Alzheimer disease 4 (3)

not provided (3)

Dilated cardiomyopathy 1V (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.028

(source)

DANN

Benign

0.39

PhyloP100

-2.5

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over