rs158898

Positions:

• chr5-168553520-A-G

Variant summary

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

The NM_024594.4(PANK3):​c.*4051T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 343,292 control chromosomes in the GnomAD database, including 24,590 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 0.37 (10408 hom., cov: 32)
  • Exomes 𝑓: 0.37 (14182 hom.)
• Consequence: PANK3 NM_024594.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.49

Genes affected

PANK3 (HGNC:19365): (pantothenate kinase 3) This gene encodes a protein belonging to the pantothenate kinase family. Pantothenate kinase is a key regulatory enzyme in the biosynthesis of coenzyme A (CoA) in bacteria and mammalian cells. It catalyzes the first committed step in the universal biosynthetic pathway leading to CoA and is itself subject to regulation through feedback inhibition by CoA. This family member is expressed most abundantly in the liver. [provided by RefSeq, Jul 2008]

SLC2A3P1 (HGNC:11008): (solute carrier family 2 member 3 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PANK3	NM_024594.4	c.*4051T>C		3_prime_UTR_variant	7/7	ENST00000239231.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PANK3	ENST00000239231.7	c.*4051T>C		3_prime_UTR_variant	7/7	1	NM_024594.4	P1
SLC2A3P1	ENST00000519666.1	n.208T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55707 AN: 151970 Hom.: 10396 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.378

GnomAD4 exome AF: 0.373 AC: 71314 AN: 191204 Hom.: 14182 Cov.: 0 AF XY: 0.382 AC XY: 40567 AN XY: 106066

Gnomad4 AFR exome AF: 0.397

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.442

Gnomad4 EAS exome AF: 0.146

Gnomad4 SAS exome AF: 0.470

Gnomad4 FIN exome AF: 0.341

Gnomad4 NFE exome AF: 0.369

Gnomad4 OTH exome AF: 0.367

GnomAD4 genome AF: 0.367 AC: 55743 AN: 152088 Hom.: 10408 Cov.: 32 AF XY: 0.362 AC XY: 26924 AN XY: 74352

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.375

Alfa AF: 0.372 Hom.: 14075

Bravo AF: 0.355

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	6.0
DANN	Benign	0.84
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs158898; hg19: chr5-167980525;