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GeneBe

rs117500254

chr10-96656894-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_152309.3(PIK3AP1):c.471C>T(p.Asp157=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000681 in 1,614,022 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00070 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00068 ( 2 hom. )

Consequence

PIK3AP1
NM_152309.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.70
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 -9 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=-0.45).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 10-96656894-G-A is Benign according to our data. Variant chr10-96656894-G-A is described in ClinVar as [Benign]. Clinvar id is 474930.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=2.7 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 106 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIK3AP1NM_152309.3 linkuse as main transcriptc.471C>T p.Asp157= synonymous_variant 3/17 ENST00000339364.10
PIK3AP1XM_011539248.2 linkuse as main transcriptc.471C>T p.Asp157= synonymous_variant 3/16
PIK3AP1XM_005269499.2 linkuse as main transcriptc.-64C>T 5_prime_UTR_variant 2/16
PIK3AP1XM_047424566.1 linkuse as main transcriptc.-64C>T 5_prime_UTR_variant 4/18

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIK3AP1ENST00000339364.10 linkuse as main transcriptc.471C>T p.Asp157= synonymous_variant 3/171 NM_152309.3 P1Q6ZUJ8-1
PIK3AP1ENST00000371110.6 linkuse as main transcriptc.-64C>T 5_prime_UTR_variant 2/162 Q6ZUJ8-2
PIK3AP1ENST00000468783.1 linkuse as main transcriptn.117C>T non_coding_transcript_exon_variant 2/85

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000697
AC:
106
AN:
152052
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000677
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000472
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000985
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.000477
AC:
120
AN:
251430
Hom.:
1
AF XY:
0.000508
AC XY:
69
AN XY:
135896
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.000347
Gnomad ASJ exome
AF:
0.000397
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.000601
Gnomad NFE exome
AF:
0.000730
Gnomad OTH exome
AF:
0.000326
GnomAD4 exome
AF:
0.000679
AC:
993
AN:
1461852
Hom.:
2
Cov.:
32
AF XY:
0.000657
AC XY:
478
AN XY:
727230
show subpopulations
Gnomad4 AFR exome
AF:
0.000448
Gnomad4 AMR exome
AF:
0.000380
Gnomad4 ASJ exome
AF:
0.000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.000824
Gnomad4 NFE exome
AF:
0.000790
Gnomad4 OTH exome
AF:
0.000431
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000697
AC:
106
AN:
152170
Hom.:
1
Cov.:
31
AF XY:
0.000565
AC XY:
42
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.000675
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000472
Gnomad4 NFE
AF:
0.000985
Gnomad4 OTH
AF:
0.000475
Alfa
AF:
0.000824
Hom.:
0
Bravo
AF:
0.000582
EpiCase
AF:
0.000872
EpiControl
AF:
0.000771

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Infantile spasms Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 22, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.45
Cadd
Benign
14
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: rs117500254; hg19: chr10-98416651; COSMIC: COSV100226220; API