rs786870

Positions:

• chr10-26485765-T-C

Variant summary

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

The NM_019043.4(APBB1IP):​c.1-6562T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,212 control chromosomes in the GnomAD database, including 50,532 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 0.81 (50532 hom., cov: 33)
• Consequence: APBB1IP NM_019043.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APBB1IP	NM_019043.4	c.1-6562T>C		intron_variant		ENST00000376236.9	NP_061916.3
APBB1IP	XM_011519514.3	c.1-6562T>C		intron_variant			XP_011517816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APBB1IP	ENST00000376236.9	c.1-6562T>C		intron_variant		5	NM_019043.4	ENSP00000365411	P1
APBB1IP	ENST00000356785.4	c.1-6562T>C		intron_variant		1		ENSP00000349237

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123310 AN: 152094 Hom.: 50464 Cov.: 33

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.811 AC: 123435 AN: 152212 Hom.: 50532 Cov.: 33 AF XY: 0.816 AC XY: 60712 AN XY: 74424

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.836

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.790

Alfa AF: 0.758 Hom.: 92426

Bravo AF: 0.814

Asia WGS AF: 0.858 AC: 2981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.67

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: rs786870; hg19: chr10-26774694;