chr9-69621565-G-A

Variant names:

• chr9-69621565-G-A
• rs11139519
• NM_001163.4:c.-70+50588C>T

Variant summary

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

The NM_001163.4(APBA1):​c.-70+50588C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,080 control chromosomes in the GnomAD database, including 1,654 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 0.13 (1654 hom., cov: 33)
• Consequence: APBA1 NM_001163.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.31
• Publications: 4 publications found

Genes affected

APBA1 (HGNC:578): (amyloid beta precursor protein binding family A member 1) The protein encoded by this gene is a member of the X11 protein family. It is a neuronal adapter protein that interacts with the Alzheimer's disease amyloid precursor protein (APP). It stabilizes APP and inhibits production of proteolytic APP fragments including the A beta peptide that is deposited in the brains of Alzheimer's disease patients. This gene product is believed to be involved in signal transduction processes. It is also regarded as a putative vesicular trafficking protein in the brain that can form a complex with the potential to couple synaptic vesicle exocytosis to neuronal cell adhesion. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001163.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APBA1	NM_001163.4	MANE Select	c.-70+50588C>T		intron	N/A	NP_001154.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APBA1	ENST00000265381.7	TSL:1 MANE Select	c.-70+50588C>T		intron	N/A	ENSP00000265381.3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19620 AN: 151960 Hom.: 1643 Cov.: 33

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0677

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.129 AC: 19644 AN: 152080 Hom.: 1654 Cov.: 33 AF XY: 0.127 AC XY: 9454 AN XY: 74326

African (AFR) AF: 0.0383 AC: 1592 AN: 41516

American (AMR) AF: 0.217 AC: 3311 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 371 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1266 AN: 5168

South Asian (SAS) AF: 0.0684 AC: 327 AN: 4784

European-Finnish (FIN) AF: 0.109 AC: 1158 AN: 10576

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11029 AN: 67982

Other (OTH) AF: 0.147 AC: 310 AN: 2110

Alfa AF: 0.144 Hom.: 2453

Bravo AF: 0.137

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.74
PhyloP100		3.3
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: rs11139519; hg19: chr9-72236481;