dbSNP rs880348: PIK3AP1:c.1736-1132G>A (chr10-96621689-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_152309.3(PIK3AP1):c.1736-1132G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,238 control chromosomes in the GnomAD database, including 12,360 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 0.40 ( 12342 hom., cov: 32)

Exomes 𝑓: 0.44 ( 18 hom. )

Consequence

PIK3AP1
NM_152309.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.05

Publications

0 publications found

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]

PIK3AP1 links:

RPS2P36 (HGNC:36784): (ribosomal protein S2 pseudogene 36)

RPS2P36 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152309.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3AP1	NM_152309.3	MANE Select	c.1736-1132G>A		intron	N/A	NP_689522.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PIK3AP1	ENST00000339364.10	TSL:1 MANE Select	c.1736-1132G>A	intron	N/A	ENSP00000339826.5	Q6ZUJ8-1
PIK3AP1	ENST00000371109.3	TSL:1	c.533-1132G>A	intron	N/A	ENSP00000360150.3	Q6ZUJ8-3
PIK3AP1	ENST00000866991.1		c.1736-1132G>A	intron	N/A	ENSP00000537050.1

Frequencies

GnomAD3 genomes

AF:

0.398

AC:

60494

AN:

151946

Hom.:

12340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.453

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.485

Gnomad FIN

AF:

0.351

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.401

Gnomad OTH

AF:

0.428

GnomAD4 exome

AF:

0.436

AC:

AN:

172

Hom.:

Cov.:

AF XY:

0.471

AC XY:

AN XY:

102

show subpopulations

African (AFR)

AF:

0.375

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.466

AC:

AN:

116

Other (OTH)

AF:

0.417

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.524

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.398

AC:

60523

AN:

152066

Hom.:

12342

Cov.:

AF XY:

0.399

AC XY:

29665

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.374

AC:

15510

AN:

41480

American (AMR)

AF:

0.453

AC:

6909

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.531

AC:

1844

AN:

3470

East Asian (EAS)

AF:

0.329

AC:

1698

AN:

5168

South Asian (SAS)

AF:

0.485

AC:

2337

AN:

4820

European-Finnish (FIN)

AF:

0.351

AC:

3716

AN:

10576

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.401

AC:

27222

AN:

67968

Other (OTH)

AF:

0.428

AC:

904

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1888

3777

5665

7554

9442

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

590

1180

1770

2360

2950

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.415

Hom.:

17008

Bravo

AF:

0.405

Asia WGS

AF:

0.452

AC:

1572

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

5.7

(source)

DANN

Benign

0.79

PhyloP100

2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over