rs2837990

chr21-41248222-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012105.5(BACE2):c.984+2159G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,096 control chromosomes in the GnomAD database, including 5,269 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 0.25 (5269 hom., cov: 32)
• Consequence: BACE2 NM_012105.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

Genes affected

BACE2 (HGNC:934): (beta-secretase 2) This gene encodes an integral membrane glycoprotein that functions as an aspartic protease. The encoded protein cleaves amyloid precursor protein into amyloid beta peptide, which is a critical step in the etiology of Alzheimer's disease and Down syndrome. The protein precursor is further processed into an active mature peptide. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BACE2	NM_012105.5	c.984+2159G>A		intron_variant		ENST00000330333.11
BACE2	NM_138991.3	c.984+2159G>A		intron_variant
BACE2	NM_138992.3	c.984+2159G>A		intron_variant
BACE2	XM_017028314.2	c.699+2159G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BACE2	ENST00000330333.11	c.984+2159G>A		intron_variant		1	NM_012105.5	P1

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37585 AN: 151978 Hom.: 5259 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.248 AC: 37648 AN: 152096 Hom.: 5269 Cov.: 32 AF XY: 0.246 AC XY: 18255 AN XY: 74340

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.245

Alfa AF: 0.201 Hom.: 6540

Bravo AF: 0.258

Asia WGS AF: 0.241 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.31
Dann	Benign	0.67

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: rs2837990; hg19: chr21-42620149;