8-9327181-T-C

Variant summary

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

The ENST00000520390.1(PPP1R3B-DT):​n.765+878T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,234 control chromosomes in the GnomAD database, including 59,420 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 0.88 ( 59420 hom., cov: 32)

Consequence

PPP1R3B-DT
ENST00000520390.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.453
Variant links:
Genes affected
PPP1R3B-DT (HGNC:56150): (PPP1R3B divergent transcript)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
LOC157273NR_040039.1 linkn.765+878T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PPP1R3B-DTENST00000518619.1 linkn.196+878T>C intron_variant 3
PPP1R3B-DTENST00000520255.6 linkn.739+878T>C intron_variant 3
PPP1R3B-DTENST00000520390.1 linkn.765+878T>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.882
AC:
134149
AN:
152116
Hom.:
59393
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.877
Gnomad AMI
AF:
0.956
Gnomad AMR
AF:
0.789
Gnomad ASJ
AF:
0.940
Gnomad EAS
AF:
0.987
Gnomad SAS
AF:
0.888
Gnomad FIN
AF:
0.823
Gnomad MID
AF:
0.930
Gnomad NFE
AF:
0.902
Gnomad OTH
AF:
0.882
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.882
AC:
134230
AN:
152234
Hom.:
59420
Cov.:
32
AF XY:
0.877
AC XY:
65291
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.877
Gnomad4 AMR
AF:
0.789
Gnomad4 ASJ
AF:
0.940
Gnomad4 EAS
AF:
0.987
Gnomad4 SAS
AF:
0.888
Gnomad4 FIN
AF:
0.823
Gnomad4 NFE
AF:
0.902
Gnomad4 OTH
AF:
0.878
Alfa
AF:
0.908
Hom.:
71552
Bravo
AF:
0.876
Asia WGS
AF:
0.923
AC:
3213
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.0
DANN
Benign
0.72

Splicing

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: rs6601299; hg19: chr8-9184691; API