X-27460603-C-T

Variant summary

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

The NM_207319.4(PPP4R3C):c.*195G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. 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 0.55 (13060 hom., 18126 hem., cov: 22)
  • Exomes 𝑓: 0.66 (30632 hom. 37735 hem.)
  • Failed GnomAD Quality Control
• Consequence: PPP4R3C NM_207319.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

Genes affected

PPP4R3C (HGNC:33146): (protein phosphatase 4 regulatory subunit 3C)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PPP4R3C	NM_207319.4	c.*195G>A		3_prime_UTR_variant	1/1	ENST00000412172.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PPP4R3C	ENST00000412172.4	c.*195G>A		3_prime_UTR_variant	1/1		NM_207319.4	P1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 60622 AN: 109957 Hom.: 13056 Cov.: 22 AF XY: 0.561 AC XY: 18110 AN XY: 32309

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.570

GnomAD4 exome AF: 0.656 AC: 130021 AN: 198127 Hom.: 30632 Cov.: 0 AF XY: 0.669 AC XY: 37735 AN XY: 56433

Gnomad4 AFR exome AF: 0.260

Gnomad4 AMR exome AF: 0.677

Gnomad4 ASJ exome AF: 0.616

Gnomad4 EAS exome AF: 0.608

Gnomad4 SAS exome AF: 0.764

Gnomad4 FIN exome AF: 0.674

Gnomad4 NFE exome AF: 0.679

Gnomad4 OTH exome AF: 0.621

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.551 AC: 60638 AN: 110012 Hom.: 13060 Cov.: 22 AF XY: 0.560 AC XY: 18126 AN XY: 32374

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.596

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.574

Alfa AF: 0.513 Hom.: 5626

Bravo AF: 0.534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.14
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5926442; hg19: chrX-27478720;