rs787041

Positions:

• chr10-26498862-T-A
• chr10-26498862-T-C
• chr10-26498862-T-G

Variant summary

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

The NM_019043.4(APBB1IP):​c.161-1957T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,140 control chromosomes in the GnomAD database, including 27,421 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 0.57 (27421 hom., cov: 32)
• Consequence: APBB1IP NM_019043.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APBB1IP	NM_019043.4	c.161-1957T>A		intron_variant		ENST00000376236.9
APBB1IP	XM_011519514.3	c.161-1957T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APBB1IP	ENST00000376236.9	c.161-1957T>A		intron_variant		5	NM_019043.4	P1
APBB1IP	ENST00000356785.4	c.161-1957T>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86763 AN: 152022 Hom.: 27352 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.571 AC: 86891 AN: 152140 Hom.: 27421 Cov.: 32 AF XY: 0.576 AC XY: 42848 AN XY: 74388

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.544

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.551

Alfa AF: 0.497 Hom.: 2571

Bravo AF: 0.589

Asia WGS AF: 0.769 AC: 2671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.75

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: rs787041; hg19: chr10-26787791;