GeneBe

rs787041

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.316
Variant links:
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]

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ACMG classification

Classification made for transcript

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 Protein UniProt
APBB1IPNM_019043.4 linkuse as main transcriptc.161-1957T>A intron_variant ENST00000376236.9 NP_061916.3
APBB1IPXM_011519514.3 linkuse as main transcriptc.161-1957T>A intron_variant XP_011517816.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
APBB1IPENST00000376236.9 linkuse as main transcriptc.161-1957T>A intron_variant 5 NM_019043.4 ENSP00000365411 P1Q7Z5R6-1
APBB1IPENST00000356785.4 linkuse as main transcriptc.161-1957T>A intron_variant 1 ENSP00000349237 Q7Z5R6-2

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs787041; hg19: chr10-26787791; API