rs1932253

Variant summary

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

The NM_019043.4(APBB1IP):​c.-1+1331A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,960 control chromosomes in the GnomAD database, including 11,645 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 0.39 ( 11645 hom., cov: 32)

Consequence

APBB1IP
NM_019043.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.330
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=-0.82).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
APBB1IPNM_019043.4 linkuse as main transcriptc.-1+1331A>G intron_variant ENST00000376236.9 NP_061916.3 Q7Z5R6-1
APBB1IPXM_011519514.3 linkuse as main transcriptc.-1+1331A>G intron_variant XP_011517816.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
APBB1IPENST00000376236.9 linkuse as main transcriptc.-1+1331A>G intron_variant 5 NM_019043.4 ENSP00000365411.4 Q7Z5R6-1
APBB1IPENST00000356785.4 linkuse as main transcriptc.-1+1331A>G intron_variant 1 ENSP00000349237.4 Q7Z5R6-2

Frequencies

GnomAD3 genomes
AF:
0.388
AC:
58931
AN:
151842
Hom.:
11629
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.447
Gnomad AMI
AF:
0.292
Gnomad AMR
AF:
0.457
Gnomad ASJ
AF:
0.358
Gnomad EAS
AF:
0.431
Gnomad SAS
AF:
0.494
Gnomad FIN
AF:
0.360
Gnomad MID
AF:
0.453
Gnomad NFE
AF:
0.333
Gnomad OTH
AF:
0.388
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.388
AC:
58993
AN:
151960
Hom.:
11645
Cov.:
32
AF XY:
0.393
AC XY:
29217
AN XY:
74250
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.456
Gnomad4 ASJ
AF:
0.358
Gnomad4 EAS
AF:
0.430
Gnomad4 SAS
AF:
0.493
Gnomad4 FIN
AF:
0.360
Gnomad4 NFE
AF:
0.333
Gnomad4 OTH
AF:
0.395
Alfa
AF:
0.365
Hom.:
1290
Bravo
AF:
0.395
Asia WGS
AF:
0.474
AC:
1642
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.1
DANN
Benign
0.61

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: rs1932253; hg19: chr10-26729113; API