rs459311

Variant names:

• chr9-125189931-G-A
• rs459311
• ENST00000451402.5:c.-213C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-125189931-G-A
• chr9-125189931-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000451402.5(PPP6C):​c.-213C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000243 in 411,354 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000024 (0 hom.)
• Consequence: PPP6C ENST00000451402.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 0 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]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451402.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP6C	NM_002721.5	MANE Select	c.-213C>T		upstream_gene	N/A	NP_002712.1
	PPP6C	NM_001123355.2		c.-213C>T		upstream_gene	N/A	NP_001116827.1
	PPP6C	NM_001123369.2		c.-213C>T		upstream_gene	N/A	NP_001116841.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP6C	ENST00000451402.5	TSL:2	c.-213C>T		5_prime_UTR	Exon 1 of 8	ENSP00000392147.1
	PPP6C	ENST00000415905.5	TSL:2	c.-213C>T		5_prime_UTR	Exon 1 of 6	ENSP00000411744.1
	PPP6C	ENST00000373547.9	TSL:1 MANE Select	c.-213C>T		upstream_gene	N/A	ENSP00000362648.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000243 AC: 1 AN: 411354 Hom.: 0 Cov.: 5 AF XY: 0.00000463 AC XY: 1 AN XY: 216132

African (AFR) AF: 0.00 AC: 0 AN: 8110

American (AMR) AF: 0.0000826 AC: 1 AN: 12106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11974

East Asian (EAS) AF: 0.00 AC: 0 AN: 23996

South Asian (SAS) AF: 0.00 AC: 0 AN: 40322

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 27528

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1812

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 261928

Other (OTH) AF: 0.00 AC: 0 AN: 23578

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.53
DANN	Benign	0.93
PhyloP100		-1.9
PromoterAI		-0.062	Neutral

Splicing

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

Other links and lift over

dbSNP: rs459311; hg19: chr9-127952210;