10-96620487-C-T

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_152309.3(PIK3AP1):​c.1806G>A​(p.Thr602Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00109 in 1,614,030 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 Benign (★★).

Frequency

Genomes: 𝑓 0.00068 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0011 ( 1 hom. )

Consequence

PIK3AP1
NM_152309.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.89
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 -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 10-96620487-C-T is Benign according to our data. Variant chr10-96620487-C-T is described in ClinVar as [Benign]. Clinvar id is 474918.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-3.89 with no splicing effect.
BS2
High AC in GnomAd4 at 104 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PIK3AP1NM_152309.3 linkc.1806G>A p.Thr602Thr synonymous_variant Exon 12 of 17 ENST00000339364.10 NP_689522.2 Q6ZUJ8-1Q86YV3
PIK3AP1XM_011539248.2 linkc.1806G>A p.Thr602Thr synonymous_variant Exon 12 of 16 XP_011537550.1
PIK3AP1XM_005269499.2 linkc.1272G>A p.Thr424Thr synonymous_variant Exon 11 of 16 XP_005269556.1 Q6ZUJ8-2
PIK3AP1XM_047424566.1 linkc.1272G>A p.Thr424Thr synonymous_variant Exon 13 of 18 XP_047280522.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PIK3AP1ENST00000339364.10 linkc.1806G>A p.Thr602Thr synonymous_variant Exon 12 of 17 1 NM_152309.3 ENSP00000339826.5 Q6ZUJ8-1
PIK3AP1ENST00000371109.3 linkc.603G>A p.Thr201Thr synonymous_variant Exon 5 of 10 1 ENSP00000360150.3 Q6ZUJ8-3
PIK3AP1ENST00000371110.6 linkc.1272G>A p.Thr424Thr synonymous_variant Exon 11 of 16 2 ENSP00000360151.2 Q6ZUJ8-2
PIK3AP1ENST00000489982.1 linkn.-76G>A upstream_gene_variant 3

Frequencies

GnomAD3 genomes
AF:
0.000684
AC:
104
AN:
152138
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000786
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00101
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.000677
AC:
170
AN:
251234
Hom.:
0
AF XY:
0.000656
AC XY:
89
AN XY:
135768
show subpopulations
Gnomad AFR exome
AF:
0.000369
Gnomad AMR exome
AF:
0.000983
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000653
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00107
Gnomad OTH exome
AF:
0.000815
GnomAD4 exome
AF:
0.00114
AC:
1660
AN:
1461774
Hom.:
1
Cov.:
34
AF XY:
0.00114
AC XY:
827
AN XY:
727190
show subpopulations
Gnomad4 AFR exome
AF:
0.000239
Gnomad4 AMR exome
AF:
0.000984
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000126
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00138
Gnomad4 OTH exome
AF:
0.00109
GnomAD4 genome
AF:
0.000683
AC:
104
AN:
152256
Hom.:
0
Cov.:
32
AF XY:
0.000699
AC XY:
52
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.000482
Gnomad4 AMR
AF:
0.000785
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00101
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00101
Hom.:
0
Bravo
AF:
0.000786
EpiCase
AF:
0.000927
EpiControl
AF:
0.00136

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Infantile spasms Benign:1
Jan 13, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.74
CADD
Benign
1.6
DANN
Benign
0.89

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: rs147512410; hg19: chr10-98380244; COSMIC: COSV59532532; COSMIC: COSV59532532; API