rs1932253

Variant names:

• chr10-26440184-A-G
• rs1932253
• NM_019043.4:c.-1+1331A>G

Variant summary

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

The NM_019043.4(APBB1IP):​c.-1+1331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,960 control chromosomes in the GnomAD database, including 11,645 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 0.39 (11645 hom., cov: 32)
• Consequence: APBB1IP NM_019043.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 1 publications found

Genes affected

APBB1IP (HGNC:17379): (amyloid beta precursor protein binding family B member 1 interacting protein) Predicted to be involved in signal transduction. Predicted to act upstream of or within T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell and positive regulation of cell adhesion. Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APBB1IP	NM_019043.4	c.-1+1331A>G		intron_variant	Intron 2 of 14	ENST00000376236.9	NP_061916.3
APBB1IP	XM_011519514.3	c.-1+1331A>G		intron_variant	Intron 2 of 13		XP_011517816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APBB1IP	ENST00000376236.9	c.-1+1331A>G		intron_variant	Intron 2 of 14	5	NM_019043.4	ENSP00000365411.4
APBB1IP	ENST00000356785.4	c.-1+1331A>G		intron_variant	Intron 2 of 4	1		ENSP00000349237.4
APBB1IP	ENST00000718302.1	c.-1+1331A>G		intron_variant	Intron 2 of 14			ENSP00000520735.1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58931 AN: 151842 Hom.: 11629 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.388 AC: 58993 AN: 151960 Hom.: 11645 Cov.: 32 AF XY: 0.393 AC XY: 29217 AN XY: 74250

African (AFR) AF: 0.447 AC: 18519 AN: 41400

American (AMR) AF: 0.456 AC: 6970 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3464

East Asian (EAS) AF: 0.430 AC: 2226 AN: 5180

South Asian (SAS) AF: 0.493 AC: 2372 AN: 4812

European-Finnish (FIN) AF: 0.360 AC: 3791 AN: 10544

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22640 AN: 67964

Other (OTH) AF: 0.395 AC: 836 AN: 2114

Alfa AF: 0.369 Hom.: 1371

Bravo AF: 0.395

Asia WGS AF: 0.474 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.61
PhyloP100		0.33
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: rs1932253; hg19: chr10-26729113;