10-96602305-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2

The NM_152309.3(PIK3AP1):​c.2335G>A​(p.Val779Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00035 in 1,607,246 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00031 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00035 ( 1 hom. )

Consequence

PIK3AP1
NM_152309.3 missense

Scores

7
12

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: 2.01
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.07975295).
BP6
Variant 10-96602305-C-T is Benign according to our data. Variant chr10-96602305-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 707691.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}.
BS2
High AC in GnomAd4 at 47 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PIK3AP1NM_152309.3 linkuse as main transcriptc.2335G>A p.Val779Met missense_variant 16/17 ENST00000339364.10 NP_689522.2
LOC105378443XR_946220.4 linkuse as main transcriptn.1447-5371C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PIK3AP1ENST00000339364.10 linkuse as main transcriptc.2335G>A p.Val779Met missense_variant 16/171 NM_152309.3 ENSP00000339826 P1Q6ZUJ8-1
PIK3AP1ENST00000371109.3 linkuse as main transcriptc.1132G>A p.Val378Met missense_variant 9/101 ENSP00000360150 Q6ZUJ8-3
PIK3AP1ENST00000371110.6 linkuse as main transcriptc.1801G>A p.Val601Met missense_variant 15/162 ENSP00000360151 Q6ZUJ8-2
PIK3AP1ENST00000467625.5 linkuse as main transcriptn.532G>A non_coding_transcript_exon_variant 5/63

Frequencies

GnomAD3 genomes
AF:
0.000302
AC:
46
AN:
152126
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000529
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000393
AC:
96
AN:
244474
Hom.:
1
AF XY:
0.000408
AC XY:
54
AN XY:
132394
show subpopulations
Gnomad AFR exome
AF:
0.000125
Gnomad AMR exome
AF:
0.0000309
Gnomad ASJ exome
AF:
0.000615
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000342
Gnomad FIN exome
AF:
0.000464
Gnomad NFE exome
AF:
0.000681
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000355
AC:
516
AN:
1455002
Hom.:
1
Cov.:
30
AF XY:
0.000344
AC XY:
249
AN XY:
723952
show subpopulations
Gnomad4 AFR exome
AF:
0.0000910
Gnomad4 AMR exome
AF:
0.0000235
Gnomad4 ASJ exome
AF:
0.000425
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.000769
Gnomad4 NFE exome
AF:
0.000393
Gnomad4 OTH exome
AF:
0.000383
GnomAD4 genome
AF:
0.000309
AC:
47
AN:
152244
Hom.:
0
Cov.:
32
AF XY:
0.000255
AC XY:
19
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.000169
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.000529
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000405
Hom.:
0
Bravo
AF:
0.000234
TwinsUK
AF:
0.000809
AC:
3
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.000681
AC:
3
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.000535
AC:
65
EpiCase
AF:
0.000273
EpiControl
AF:
0.000594

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsOct 12, 2022The c.2335G>A (p.V779M) alteration is located in exon 16 (coding exon 16) of the PIK3AP1 gene. This alteration results from a G to A substitution at nucleotide position 2335, causing the valine (V) at amino acid position 779 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Infantile spasms Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 16, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.45
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.38
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.21
T;.;.
Eigen
Uncertain
0.25
Eigen_PC
Benign
0.21
FATHMM_MKL
Benign
0.50
N
LIST_S2
Uncertain
0.93
D;D;D
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.080
T;T;T
MetaSVM
Benign
-0.88
T
MutationAssessor
Benign
1.2
L;.;.
MutationTaster
Benign
0.75
D;D;D
PrimateAI
Uncertain
0.61
T
PROVEAN
Benign
-0.92
N;N;N
REVEL
Benign
0.11
Sift
Uncertain
0.021
D;D;D
Sift4G
Uncertain
0.020
D;D;D
Polyphen
0.94
P;.;D
Vest4
0.34
MVP
0.40
MPC
1.4
ClinPred
0.066
T
GERP RS
3.0
Varity_R
0.053
gMVP
0.22

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: rs45587542; hg19: chr10-98362062; API