rs787041

Variant names:

• chr10-26498862-T-A
• rs787041
• NM_019043.4:c.161-1957T>A

Your query was ambiguous. Multiple possible variants found:

• chr10-26498862-T-A
• chr10-26498862-T-C
• chr10-26498862-T-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.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
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
APBB1IP	NM_019043.4	c.161-1957T>A		intron_variant	Intron 4 of 14	ENST00000376236.9	NP_061916.3
APBB1IP	XM_011519514.3	c.161-1957T>A		intron_variant	Intron 4 of 13		XP_011517816.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APBB1IP	ENST00000376236.9	c.161-1957T>A		intron_variant	Intron 4 of 14	5	NM_019043.4	ENSP00000365411.4
APBB1IP	ENST00000356785.4	c.161-1957T>A		intron_variant	Intron 4 of 4	1		ENSP00000349237.4
APBB1IP	ENST00000718302.1	c.161-1957T>A		intron_variant	Intron 4 of 14			ENSP00000520735.1

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

African (AFR) AF: 0.828 AC: 34379 AN: 41522

American (AMR) AF: 0.544 AC: 8308 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3470

East Asian (EAS) AF: 0.872 AC: 4521 AN: 5182

South Asian (SAS) AF: 0.680 AC: 3281 AN: 4828

European-Finnish (FIN) AF: 0.488 AC: 5164 AN: 10582

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28054 AN: 67956

Other (OTH) AF: 0.551 AC: 1162 AN: 2110

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
PhyloP100		-0.32
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: rs787041; hg19: chr10-26787791;