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GeneBe

rs1436186

Positions:

Variant summary

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

The NM_152309.3(PIK3AP1):​c.430+7986T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,088 control chromosomes in the GnomAD database, including 20,722 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 0.52 ( 20722 hom., cov: 33)

Consequence

PIK3AP1
NM_152309.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.626
Variant links:
Genes affected
PIK3AP1 (HGNC:30034): (phosphoinositide-3-kinase adaptor protein 1) Predicted to enable phosphatidylinositol 3-kinase regulatory subunit binding activity and signaling receptor binding activity. Predicted to be involved in regulation of inflammatory response; regulation of signal transduction; and toll-like receptor signaling pathway. Predicted to be located in cytoplasm and membrane. Predicted to be active in cytosol. [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
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIK3AP1NM_152309.3 linkuse as main transcriptc.430+7986T>C intron_variant ENST00000339364.10
PIK3AP1XM_011539248.2 linkuse as main transcriptc.430+7986T>C intron_variant
PIK3AP1XM_047424566.1 linkuse as main transcriptc.-105+7986T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIK3AP1ENST00000339364.10 linkuse as main transcriptc.430+7986T>C intron_variant 1 NM_152309.3 P1Q6ZUJ8-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.519
AC:
78871
AN:
151970
Hom.:
20696
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.567
Gnomad AMI
AF:
0.471
Gnomad AMR
AF:
0.544
Gnomad ASJ
AF:
0.578
Gnomad EAS
AF:
0.566
Gnomad SAS
AF:
0.598
Gnomad FIN
AF:
0.464
Gnomad MID
AF:
0.665
Gnomad NFE
AF:
0.479
Gnomad OTH
AF:
0.553
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.519
AC:
78937
AN:
152088
Hom.:
20722
Cov.:
33
AF XY:
0.520
AC XY:
38690
AN XY:
74350
show subpopulations
Gnomad4 AFR
AF:
0.567
Gnomad4 AMR
AF:
0.544
Gnomad4 ASJ
AF:
0.578
Gnomad4 EAS
AF:
0.567
Gnomad4 SAS
AF:
0.597
Gnomad4 FIN
AF:
0.464
Gnomad4 NFE
AF:
0.479
Gnomad4 OTH
AF:
0.559
Alfa
AF:
0.313
Hom.:
691
Bravo
AF:
0.529
Asia WGS
AF:
0.599
AC:
2086
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
1.3
DANN
Benign
0.55

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: rs1436186; hg19: chr10-98461338; API