15-75090201-G-T

Variant names:

• chr15-75090201-G-T
• rs12148488
• ENST00000563298.1:n.134-26919G>T

Variant summary

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

The ENST00000563298.1(PPCDC):​n.134-26919G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 152,062 control chromosomes in the GnomAD database, including 22,245 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 0.54 (22245 hom., cov: 32)
• Consequence: PPCDC ENST00000563298.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563
• Publications: 20 publications found

Genes affected

PPCDC (HGNC:28107): (phosphopantothenoylcysteine decarboxylase) Biosynthesis of coenzyme A (CoA) from pantothenic acid (vitamin B5) is an essential universal pathway in prokaryotes and eukaryotes. PPCDC (EC 4.1.1.36), one of the last enzymes in this pathway, converts phosphopantothenoylcysteine to 4-prime-phosphopantetheine (Daugherty et al., 2002 [PubMed 11923312]).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563298.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPCDC	ENST00000563298.1	TSL:5	n.134-26919G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81291 AN: 151944 Hom.: 22219 Cov.: 32

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.559

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.535 AC: 81362 AN: 152062 Hom.: 22245 Cov.: 32 AF XY: 0.547 AC XY: 40671 AN XY: 74308

African (AFR) AF: 0.503 AC: 20882 AN: 41484

American (AMR) AF: 0.505 AC: 7716 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1947 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4225 AN: 5176

South Asian (SAS) AF: 0.815 AC: 3932 AN: 4826

European-Finnish (FIN) AF: 0.585 AC: 6168 AN: 10550

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34606 AN: 67970

Other (OTH) AF: 0.556 AC: 1175 AN: 2112

Alfa AF: 0.520 Hom.: 49762

Bravo AF: 0.520

Asia WGS AF: 0.765 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.76
DANN	Benign	0.48
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs12148488; hg19: chr15-75382542;