X-27460603-C-T

Variant names:

• chrX-27460603-C-T
• rs5926442
• NM_207319.4:c.*195G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412172.4(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 ENST00000412172.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412172.4. 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
	PPP4R3C	NM_207319.4	MANE Select	c.*195G>A		3_prime_UTR	Exon 1 of 1	NP_997202.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP4R3C	ENST00000412172.4	TSL:6 MANE Select	c.*195G>A		3_prime_UTR	Exon 1 of 1	ENSP00000489770.1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 60622 AN: 109957 Hom.: 13056 Cov.: 22

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

African (AFR) AF: 0.260 AC: 1429 AN: 5505

American (AMR) AF: 0.677 AC: 4726 AN: 6982

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 4071 AN: 6609

East Asian (EAS) AF: 0.608 AC: 10177 AN: 16736

South Asian (SAS) AF: 0.764 AC: 4061 AN: 5317

European-Finnish (FIN) AF: 0.674 AC: 10274 AN: 15239

Middle Eastern (MID) AF: 0.534 AC: 485 AN: 909

European-Non Finnish (NFE) AF: 0.679 AC: 86639 AN: 127689

Other (OTH) AF: 0.621 AC: 8159 AN: 13141

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

African (AFR) AF: 0.257 AC: 7812 AN: 30408

American (AMR) AF: 0.639 AC: 6614 AN: 10357

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 1636 AN: 2616

East Asian (EAS) AF: 0.596 AC: 2034 AN: 3411

South Asian (SAS) AF: 0.759 AC: 1979 AN: 2608

European-Finnish (FIN) AF: 0.670 AC: 3801 AN: 5671

Middle Eastern (MID) AF: 0.507 AC: 106 AN: 209

European-Non Finnish (NFE) AF: 0.674 AC: 35438 AN: 52567

Other (OTH) AF: 0.574 AC: 862 AN: 1503

Alfa AF: 0.513 Hom.: 5626

Bravo AF: 0.534

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.69
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs5926442; hg19: chrX-27478720;