rs1775230

Positions:

• chr10-26517700-A-G
• chr10-26517700-A-T

Variant summary

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

The NM_019043.4(APBB1IP):​c.813+4040A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,300 control chromosomes in the GnomAD database, including 53,231 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 0.83 (53231 hom., cov: 34)
• Consequence: APBB1IP NM_019043.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APBB1IP	NM_019043.4	c.813+4040A>G		intron_variant		ENST00000376236.9	NP_061916.3
APBB1IP	XM_011519514.3	c.813+4040A>G		intron_variant			XP_011517816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APBB1IP	ENST00000376236.9	c.813+4040A>G		intron_variant		5	NM_019043.4	ENSP00000365411.4

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126935 AN: 152182 Hom.: 53197 Cov.: 34

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.834 AC: 127019 AN: 152300 Hom.: 53231 Cov.: 34 AF XY: 0.836 AC XY: 62222 AN XY: 74470

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.864

Gnomad4 OTH AF: 0.827

Alfa AF: 0.854 Hom.: 48867

Bravo AF: 0.831

Asia WGS AF: 0.860 AC: 2992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.6
DANN	Benign	0.39

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: rs1775230; hg19: chr10-26806629;