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GeneBe

rs6677649

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005026.5(PIK3CD):​c.-137-5277A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 151,964 control chromosomes in the GnomAD database, including 1,939 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 0.14 ( 1939 hom., cov: 31)

Consequence

PIK3CD
NM_005026.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.355
Variant links:
Genes affected
PIK3CD (HGNC:8977): (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta) Phosphoinositide 3-kinases (PI3Ks) phosphorylate inositol lipids and are involved in the immune response. The protein encoded by this gene is a class I PI3K found primarily in leukocytes. Like other class I PI3Ks (p110-alpha p110-beta, and p110-gamma), the encoded protein binds p85 adapter proteins and GTP-bound RAS. However, unlike the other class I PI3Ks, this protein phosphorylates itself, not p85 protein.[provided by RefSeq, Jul 2010]
PIK3CD-AS2 (HGNC:51334): (PIK3CD antisense RNA 2)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PIK3CDNM_005026.5 linkuse as main transcriptc.-137-5277A>G intron_variant ENST00000377346.9
PIK3CD-AS2NR_126367.1 linkuse as main transcriptn.240+1145T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PIK3CDENST00000377346.9 linkuse as main transcriptc.-137-5277A>G intron_variant 1 NM_005026.5 P3O00329-1
PIK3CD-AS2ENST00000415330.4 linkuse as main transcriptn.249+1145T>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.143
AC:
21653
AN:
151848
Hom.:
1924
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.221
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.152
Gnomad EAS
AF:
0.146
Gnomad SAS
AF:
0.251
Gnomad FIN
AF:
0.0930
Gnomad MID
AF:
0.156
Gnomad NFE
AF:
0.0803
Gnomad OTH
AF:
0.136
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.143
AC:
21710
AN:
151964
Hom.:
1939
Cov.:
31
AF XY:
0.146
AC XY:
10864
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.221
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.152
Gnomad4 EAS
AF:
0.146
Gnomad4 SAS
AF:
0.251
Gnomad4 FIN
AF:
0.0930
Gnomad4 NFE
AF:
0.0803
Gnomad4 OTH
AF:
0.141
Alfa
AF:
0.101
Hom.:
1314
Bravo
AF:
0.154
Asia WGS
AF:
0.210
AC:
729
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.59
DANN
Benign
0.63

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: rs6677649; hg19: chr1-9746248; API