21-25891809-G-A

Position:

chr21-25891809-G-A

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The ENST00000346798.8(APP):c.2124C>T(p.Gly708=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00221 in 1,613,822 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0034 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0021 ( 3 hom. )

Consequence

APP
ENST00000346798.8 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -0.832

Variant links:

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]

APP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 21-25891809-G-A is Benign according to our data. Variant chr21-25891809-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 339629.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-25891809-G-A is described in Lovd as [Benign]. Variant chr21-25891809-G-A is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-0.832 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00337 (512/152052) while in subpopulation AFR AF= 0.00752 (312/41472). AF 95% confidence interval is 0.00684. There are 2 homozygotes in gnomad4. There are 226 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 512 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APP	NM_000484.4 linkuse as main transcript	c.2124C>T	p.Gly708=	synonymous_variant	17/18	ENST00000346798.8	NP_000475.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APP	ENST00000346798.8 linkuse as main transcript	c.2124C>T	p.Gly708=	synonymous_variant	17/18	1	NM_000484.4	ENSP00000284981		P05067-1

Frequencies

GnomAD3 genomes

AF:

0.00328

AC:

499

AN:

151934

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00723

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00295

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.000833

Gnomad FIN

AF:

0.00133

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00179

Gnomad OTH

AF:

0.00335

GnomAD3 exomes

AF:

0.00189

AC:

476

AN:

251332

Hom.:

AF XY:

0.00175

AC XY:

238

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.00744

Gnomad AMR exome

AF:

0.00165

Gnomad ASJ exome

AF:

0.000198

Gnomad EAS exome

AF:

0.00169

Gnomad SAS exome

AF:

0.000523

Gnomad FIN exome

AF:

0.000508

Gnomad NFE exome

AF:

0.00196

Gnomad OTH exome

AF:

0.00245

GnomAD4 exome

AF:

0.00209

AC:

3050

AN:

1461770

Hom.:

Cov.:

AF XY:

0.00197

AC XY:

1435

AN XY:

727190

show subpopulations

Gnomad4 AFR exome

AF:

0.00747

Gnomad4 AMR exome

AF:

0.00165

Gnomad4 ASJ exome

AF:

0.000268

Gnomad4 EAS exome

AF:

0.00121

Gnomad4 SAS exome

AF:

0.000614

Gnomad4 FIN exome

AF:

0.000918

Gnomad4 NFE exome

AF:

0.00218

Gnomad4 OTH exome

AF:

0.00238

GnomAD4 genome

AF:

0.00337

AC:

512

AN:

152052

Hom.:

Cov.:

AF XY:

0.00304

AC XY:

226

AN XY:

74316

show subpopulations

Gnomad4 AFR

AF:

0.00752

Gnomad4 AMR

AF:

0.00295

Gnomad4 ASJ

AF:

0.000289

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.000833

Gnomad4 FIN

AF:

0.00133

Gnomad4 NFE

AF:

0.00179

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00229

Hom.:

Bravo

AF:

0.00352

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.00169

EpiControl

AF:

0.00213

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:5

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Nov 01, 2023	APP: BP4, BP7 -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 20, 2017	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -

Alzheimer disease

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	- -
Likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -

not specified

Benign:1

Benign, no assertion criteria provided

clinical testing

Genome Diagnostics Laboratory, Amsterdam University Medical Center

- -

APP POLYMORPHISM

Benign:1

Benign, no assertion criteria provided

literature only

OMIM

Jul 01, 1992

- -

Alzheimer disease type 1;C2751536:Cerebral amyloid angiopathy, APP-related

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jul 29, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

7.9

DANN

Benign

0.61

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over