rs1775246

chr10-26492459-G-A

Variant summary

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

The NM_019043.4(APBB1IP):c.72+61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.769 in 1,480,308 control chromosomes in the GnomAD database, including 439,933 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 0.80 (49552 hom., cov: 32)
  • Exomes 𝑓: 0.76 (390381 hom.)
• Consequence: APBB1IP NM_019043.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APBB1IP	NM_019043.4	c.72+61G>A		intron_variant		ENST00000376236.9
APBB1IP	XM_011519514.3	c.72+61G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APBB1IP	ENST00000376236.9	c.72+61G>A		intron_variant		5	NM_019043.4	P1
APBB1IP	ENST00000356785.4	c.72+61G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122209 AN: 152090 Hom.: 49490 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.784

GnomAD4 exome AF: 0.765 AC: 1015706 AN: 1328100 Hom.: 390381 AF XY: 0.766 AC XY: 511476 AN XY: 667890

Gnomad4 AFR exome AF: 0.888

Gnomad4 AMR exome AF: 0.847

Gnomad4 ASJ exome AF: 0.807

Gnomad4 EAS exome AF: 0.911

Gnomad4 SAS exome AF: 0.821

Gnomad4 FIN exome AF: 0.823

Gnomad4 NFE exome AF: 0.742

Gnomad4 OTH exome AF: 0.775

GnomAD4 genome AF: 0.804 AC: 122328 AN: 152208 Hom.: 49552 Cov.: 32 AF XY: 0.808 AC XY: 60148 AN XY: 74400

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.787

Alfa AF: 0.767 Hom.: 9125

Bravo AF: 0.806

Asia WGS AF: 0.853 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.9
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: rs1775246; hg19: chr10-26781388;