GeneBe

rs2307733

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_015316.3(PPP1R13B):​c.9+2061_9+2062insGTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.67 ( 34697 hom., cov: 0)

Consequence

PPP1R13B
NM_015316.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.235

Publications

2 publications found
Variant links:
Genes affected
PPP1R13B (HGNC:14950): (protein phosphatase 1 regulatory subunit 13B) This gene encodes a member of the ASPP (apoptosis-stimulating protein of p53) family of p53 interacting proteins. The protein contains four ankyrin repeats and an SH3 domain involved in protein-protein interactions. ASPP proteins are required for the induction of apoptosis by p53-family proteins. They promote DNA binding and transactivation of p53-family proteins on the promoters of proapoptotic genes. Expression of this gene is regulated by the E2F transcription factor. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PPP1R13BNM_015316.3 linkc.9+2061_9+2062insGTAT intron_variant Intron 1 of 16 ENST00000202556.14 NP_056131.2 Q96KQ4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PPP1R13BENST00000202556.14 linkc.9+2061_9+2062insGTAT intron_variant Intron 1 of 16 1 NM_015316.3 ENSP00000202556.9 Q96KQ4

Frequencies

GnomAD3 genomes
AF:
0.666
AC:
100825
AN:
151432
Hom.:
34628
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.860
Gnomad AMI
AF:
0.682
Gnomad AMR
AF:
0.656
Gnomad ASJ
AF:
0.563
Gnomad EAS
AF:
0.523
Gnomad SAS
AF:
0.515
Gnomad FIN
AF:
0.572
Gnomad MID
AF:
0.573
Gnomad NFE
AF:
0.593
Gnomad OTH
AF:
0.615
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.666
AC:
100952
AN:
151550
Hom.:
34697
Cov.:
0
AF XY:
0.662
AC XY:
49030
AN XY:
74024
show subpopulations
African (AFR)
AF:
0.860
AC:
35568
AN:
41336
American (AMR)
AF:
0.657
AC:
9996
AN:
15218
Ashkenazi Jewish (ASJ)
AF:
0.563
AC:
1952
AN:
3470
East Asian (EAS)
AF:
0.523
AC:
2688
AN:
5142
South Asian (SAS)
AF:
0.515
AC:
2469
AN:
4798
European-Finnish (FIN)
AF:
0.572
AC:
5986
AN:
10458
Middle Eastern (MID)
AF:
0.585
AC:
172
AN:
294
European-Non Finnish (NFE)
AF:
0.593
AC:
40211
AN:
67824
Other (OTH)
AF:
0.614
AC:
1291
AN:
2102
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1669
3338
5007
6676
8345
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
784
1568
2352
3136
3920
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.644
Hom.:
3914
Bravo
AF:
0.678
Asia WGS
AF:
0.547
AC:
1893
AN:
3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.23
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs2307733; hg19: chr14-104311574; API