Genetic Variant ENST00000451402.5:c.-213C>T (chr9-125189931-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.89

Publications

0 publications found

Variant links:

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]

PPP6C links:

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ACMG classification

Classification was made for transcript

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
PPP6C	NM_002721.5 link	c.-213C>T	upstream_gene_variant	ENST00000373547.9	NP_002712.1
PPP6C	NM_001123355.2 link	c.-213C>T	upstream_gene_variant		NP_001116827.1
PPP6C	NM_001123369.2 link	c.-213C>T	upstream_gene_variant		NP_001116841.1
PPP6C	XM_047423566.1 link	c.-213C>T	upstream_gene_variant		XP_047279522.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
PPP6C	ENST00000451402.5 link	c.-213C>T	5_prime_UTR_variant	Exon 1 of 8	2		ENSP00000392147.1
PPP6C	ENST00000415905.5 link	c.-213C>T	5_prime_UTR_variant	Exon 1 of 6	2		ENSP00000411744.1
PPP6C	ENST00000373547.9 link	c.-213C>T	upstream_gene_variant		1	NM_002721.5	ENSP00000362648.4
PPP6C	ENST00000456642.1 link	c.-342C>T	upstream_gene_variant		3		ENSP00000416287.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000243

AC:

AN:

411354

Hom.:

Cov.:

AF XY:

0.00000463

AC XY:

AN XY:

216132

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

8110

American (AMR)

AF:

0.0000826

AC:

AN:

12106

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11974

East Asian (EAS)

AF:

0.00

AC:

AN:

23996

South Asian (SAS)

AF:

0.00

AC:

AN:

40322

European-Finnish (FIN)

AF:

0.00

AC:

AN:

27528

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1812

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

261928

Other (OTH)

AF:

0.00

AC:

AN:

23578

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.53

(source)

DANN

Benign

0.93

PhyloP100

-1.9

PromoterAI

-0.062

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over