chr11-130138209-T-C

Variant names:

• chr11-130138209-T-C
• rs879780
• NM_001142276.2:c.1838-2189T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001142276.2(APLP2):​c.1838-2189T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 152,194 control chromosomes in the GnomAD database, including 10,959 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 0.28 (10959 hom., cov: 32)
• Consequence: APLP2 NM_001142276.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 8 publications found

Genes affected

APLP2 (HGNC:598): (amyloid beta precursor like protein 2) This gene encodes amyloid precursor- like protein 2 (APLP2), which is a member of the APP (amyloid precursor protein) family including APP, APLP1 and APLP2. This protein is ubiquitously expressed. It contains heparin-, copper- and zinc- binding domains at the N-terminus, BPTI/Kunitz inhibitor and E2 domains in the middle region, and transmembrane and intracellular domains at the C-terminus. This protein interacts with major histocompatibility complex (MHC) class I molecules. The synergy of this protein and the APP is required to mediate neuromuscular transmission, spatial learning and synaptic plasticity. This protein has been implicated in the pathogenesis of Alzheimer's disease. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APLP2	NM_001142276.2	c.1838-2189T>C		intron_variant	Intron 13 of 16	ENST00000338167.10	NP_001135748.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APLP2	ENST00000338167.10	c.1838-2189T>C		intron_variant	Intron 13 of 16	1	NM_001142276.2	ENSP00000345444.5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42205 AN: 152076 Hom.: 10925 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.278 AC: 42288 AN: 152194 Hom.: 10959 Cov.: 32 AF XY: 0.270 AC XY: 20108 AN XY: 74414

African (AFR) AF: 0.688 AC: 28521 AN: 41480

American (AMR) AF: 0.149 AC: 2273 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 366 AN: 3472

East Asian (EAS) AF: 0.325 AC: 1683 AN: 5186

South Asian (SAS) AF: 0.0840 AC: 405 AN: 4824

European-Finnish (FIN) AF: 0.0678 AC: 719 AN: 10604

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7627 AN: 68014

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.225 Hom.: 1334

Bravo AF: 0.308

Asia WGS AF: 0.208 AC: 722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.29
PhyloP100		0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs879780; hg19: chr11-130008104;