rs7019234

chr9-125151485-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002721.5(PPP6C):c.670-1564T>C variant causes a intron change. The variant allele was found at a frequency of 0.423 in 790,136 control chromosomes in the GnomAD database, including 73,586 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 0.44 (15267 hom., cov: 33)
  • Exomes 𝑓: 0.42 (58319 hom.)
• Consequence: PPP6C NM_002721.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.99

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]

PRPS1P2 (HGNC:9464): (phosphoribosyl pyrophosphate synthetase 1 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP6C	NM_002721.5	c.670-1564T>C		intron_variant		ENST00000373547.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP6C	ENST00000373547.9	c.670-1564T>C		intron_variant		1	NM_002721.5	P1
PRPS1P2	ENST00000430496.1	n.833A>G		non_coding_transcript_exon_variant	1/1
PPP6C	ENST00000415905.5	c.604-1564T>C		intron_variant		2
PPP6C	ENST00000451402.5	c.781-1564T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67225 AN: 151950 Hom.: 15246 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.441

GnomAD4 exome AF: 0.418 AC: 266910 AN: 638068 Hom.: 58319 Cov.: 6 AF XY: 0.420 AC XY: 145406 AN XY: 345794

Gnomad4 AFR exome AF: 0.473

Gnomad4 AMR exome AF: 0.255

Gnomad4 ASJ exome AF: 0.502

Gnomad4 EAS exome AF: 0.534

Gnomad4 SAS exome AF: 0.391

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.439

Gnomad4 OTH exome AF: 0.437

GnomAD4 genome AF: 0.442 AC: 67286 AN: 152068 Hom.: 15267 Cov.: 33 AF XY: 0.433 AC XY: 32212 AN XY: 74344

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.448

Alfa AF: 0.431 Hom.: 2994

Bravo AF: 0.451

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	9.4
Dann	Benign	0.78

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

Other links and lift over

dbSNP: rs7019234; hg19: chr9-127913764;