rs10839562

chr11-6412035-C-G

Variant summary

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

The NM_001164.5(APBB1):c.-14-674G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,204 control chromosomes in the GnomAD database, including 4,496 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 0.23 (4496 hom., cov: 33)
• Consequence: APBB1 NM_001164.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

Genes affected

APBB1 (HGNC:581): (amyloid beta precursor protein binding family B member 1) The protein encoded by this gene is a member of the Fe65 protein family. It is an adaptor protein localized in the nucleus. It interacts with the Alzheimer's disease amyloid precursor protein (APP), transcription factor CP2/LSF/LBP1 and the low-density lipoprotein receptor-related protein. APP functions as a cytosolic anchoring site that can prevent the gene product's nuclear translocation. This encoded protein could play an important role in the pathogenesis of Alzheimer's disease. It is thought to regulate transcription. Also it is observed to block cell cycle progression by downregulating thymidylate synthase expression. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APBB1	NM_001164.5	c.-14-674G>C		intron_variant		ENST00000609360.6
APBB1	NM_145689.3	c.-14-674G>C		intron_variant
APBB1	NR_047512.2	n.128-674G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APBB1	ENST00000609360.6	c.-14-674G>C		intron_variant		5	NM_001164.5	A1

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35076 AN: 152086 Hom.: 4496 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.230 AC: 35077 AN: 152204 Hom.: 4496 Cov.: 33 AF XY: 0.228 AC XY: 16996 AN XY: 74402

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.240

Alfa AF: 0.264 Hom.: 758

Bravo AF: 0.217

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.6
Dann	Benign	0.62

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: rs10839562; hg19: chr11-6433265;