chr15-63296463-G-A

Variant names:

• chr15-63296463-G-A
• rs2068143
• NM_031301.4:c.479-5882G>A

Variant summary

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

The NM_031301.4(APH1B):​c.479-5882G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,000 control chromosomes in the GnomAD database, including 12,448 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 0.37 (12448 hom., cov: 32)
• Consequence: APH1B NM_031301.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 13 publications found

Genes affected

APH1B (HGNC:24080): (aph-1 homolog B, gamma-secretase subunit) This gene encodes a multi-pass transmembrane protein that is a functional component of the gamma-secretase complex, which also contains presenilin and nicastrin. This protein represents a stabilizing cofactor for the presenilin holoprotein in the complex. The gamma-secretase complex catalyzes the cleavage of integral proteins such as notch receptors and beta-amyloid precursor protein. [provided by RefSeq, Sep 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031301.4. 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
	APH1B	NM_031301.4	MANE Select	c.479-5882G>A		intron	N/A	NP_112591.2
	APH1B	NM_001145646.2		c.356-5882G>A		intron	N/A	NP_001139118.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APH1B	ENST00000261879.10	TSL:1 MANE Select	c.479-5882G>A		intron	N/A	ENSP00000261879.5
	APH1B	ENST00000380343.8	TSL:1	c.356-5882G>A		intron	N/A	ENSP00000369700.4
	APH1B	ENST00000559971.5	TSL:1	n.*555-5882G>A		intron	N/A	ENSP00000453516.1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56356 AN: 151882 Hom.: 12419 Cov.: 32

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.371 AC: 56430 AN: 152000 Hom.: 12448 Cov.: 32 AF XY: 0.372 AC XY: 27617 AN XY: 74312

African (AFR) AF: 0.618 AC: 25597 AN: 41430

American (AMR) AF: 0.378 AC: 5776 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3466

East Asian (EAS) AF: 0.123 AC: 638 AN: 5180

South Asian (SAS) AF: 0.346 AC: 1670 AN: 4824

European-Finnish (FIN) AF: 0.291 AC: 3075 AN: 10554

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17707 AN: 67970

Other (OTH) AF: 0.336 AC: 707 AN: 2104

Alfa AF: 0.278 Hom.: 7981

Bravo AF: 0.385

Asia WGS AF: 0.241 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0040
DANN	Benign	0.64
PhyloP100		-2.3
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: rs2068143; hg19: chr15-63588662;