NM_152309.3:c.431-1239T>C

Variant names:

• chr10-96658173-A-G
• rs7098785
• NM_152309.3:c.431-1239T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152309.3(PIK3AP1):​c.431-1239T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,026 control chromosomes in the GnomAD database, including 32,436 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 0.64 (32436 hom., cov: 31)
• Consequence: PIK3AP1 NM_152309.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 11 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 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.431-1239T>C		intron	N/A	NP_689522.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PIK3AP1	ENST00000339364.10	TSL:1 MANE Select	c.431-1239T>C		intron	N/A	ENSP00000339826.5	Q6ZUJ8-1
	PIK3AP1	ENST00000866991.1		c.431-1239T>C		intron	N/A	ENSP00000537050.1
	PIK3AP1	ENST00000866992.1		c.431-1239T>C		intron	N/A	ENSP00000537051.1

Frequencies

GnomAD3 genomes AF: 0.635 AC: 96521 AN: 151910 Hom.: 32385 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.629

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.636 AC: 96627 AN: 152026 Hom.: 32436 Cov.: 31 AF XY: 0.632 AC XY: 46955 AN XY: 74308

African (AFR) AF: 0.870 AC: 36058 AN: 41458

American (AMR) AF: 0.645 AC: 9847 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2053 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3243 AN: 5176

South Asian (SAS) AF: 0.609 AC: 2933 AN: 4818

European-Finnish (FIN) AF: 0.488 AC: 5145 AN: 10552

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35416 AN: 67970

Other (OTH) AF: 0.634 AC: 1336 AN: 2108

Alfa AF: 0.574 Hom.: 48036

Bravo AF: 0.660

Asia WGS AF: 0.658 AC: 2290 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.44
PhyloP100		-2.4
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: rs7098785; hg19: chr10-98417930;