rs7019234

Variant names:

• chr9-125151485-A-G
• rs7019234
• NM_002721.5:c.670-1564T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PPP6C	NM_002721.5	c.670-1564T>C		intron_variant	Intron 6 of 6	ENST00000373547.9	NP_002712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP6C	ENST00000373547.9	c.670-1564T>C		intron_variant	Intron 6 of 6	1	NM_002721.5	ENSP00000362648.4
PRPS1P2	ENST00000430496.1	n.833A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
PPP6C	ENST00000451402.5	c.781-1564T>C		intron_variant	Intron 7 of 7	2		ENSP00000392147.1
PPP6C	ENST00000415905.5	c.604-1564T>C		intron_variant	Intron 5 of 5	2		ENSP00000411744.1

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

African (AFR) AF: 0.473 AC: 8377 AN: 17692

American (AMR) AF: 0.255 AC: 10729 AN: 42082

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 9975 AN: 19858

East Asian (EAS) AF: 0.534 AC: 19214 AN: 35956

South Asian (SAS) AF: 0.391 AC: 26456 AN: 67728

European-Finnish (FIN) AF: 0.297 AC: 15357 AN: 51756

Middle Eastern (MID) AF: 0.459 AC: 1869 AN: 4068

European-Non Finnish (NFE) AF: 0.439 AC: 160508 AN: 365922

Other (OTH) AF: 0.437 AC: 14425 AN: 33006

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

African (AFR) AF: 0.476 AC: 19726 AN: 41466

American (AMR) AF: 0.370 AC: 5647 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3468

East Asian (EAS) AF: 0.528 AC: 2726 AN: 5160

South Asian (SAS) AF: 0.411 AC: 1977 AN: 4814

European-Finnish (FIN) AF: 0.293 AC: 3102 AN: 10600

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30849 AN: 67966

Other (OTH) AF: 0.448 AC: 947 AN: 2116

Alfa AF: 0.432 Hom.: 3079

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
PhyloP100		5.0
Mutation Taster		=95/5	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7019234; hg19: chr9-127913764;