9-125153593-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_002721.5(PPP6C):c.609T>C(p.Asp203=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,614,154 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0081 ( 21 hom., cov: 32)
Exomes 𝑓: 0.00071 ( 14 hom. )
Consequence
PPP6C
NM_002721.5 synonymous
NM_002721.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.06
Genes affected
PPP6C (HGNC:9323): (protein phosphatase 6 catalytic subunit) This gene encodes the catalytic subunit of protein phosphatase, a component of a signaling pathway regulating cell cycle progression. Splice variants encoding different protein isoforms exist. The pseudogene of this gene is located on chromosome X. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 9-125153593-A-G is Benign according to our data. Variant chr9-125153593-A-G is described in ClinVar as [Benign]. Clinvar id is 720441.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.06 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00808 (1230/152266) while in subpopulation AFR AF= 0.0277 (1152/41548). AF 95% confidence interval is 0.0264. There are 21 homozygotes in gnomad4. There are 595 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1226 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PPP6C | NM_002721.5 | c.609T>C | p.Asp203= | synonymous_variant | 6/7 | ENST00000373547.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PPP6C | ENST00000373547.9 | c.609T>C | p.Asp203= | synonymous_variant | 6/7 | 1 | NM_002721.5 | P1 | |
PPP6C | ENST00000451402.5 | c.720T>C | p.Asp240= | synonymous_variant | 7/8 | 2 | |||
PPP6C | ENST00000415905.5 | c.543T>C | p.Asp181= | synonymous_variant | 5/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00806 AC: 1226AN: 152148Hom.: 21 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1226
AN:
152148
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00211 AC: 530AN: 251464Hom.: 4 AF XY: 0.00163 AC XY: 221AN XY: 135912
GnomAD3 exomes
AF:
AC:
530
AN:
251464
Hom.:
AF XY:
AC XY:
221
AN XY:
135912
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000715 AC: 1045AN: 1461888Hom.: 14 Cov.: 31 AF XY: 0.000645 AC XY: 469AN XY: 727244
GnomAD4 exome
AF:
AC:
1045
AN:
1461888
Hom.:
Cov.:
31
AF XY:
AC XY:
469
AN XY:
727244
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00808 AC: 1230AN: 152266Hom.: 21 Cov.: 32 AF XY: 0.00799 AC XY: 595AN XY: 74474
GnomAD4 genome
?
AF:
AC:
1230
AN:
152266
Hom.:
Cov.:
32
AF XY:
AC XY:
595
AN XY:
74474
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
6
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at