5-168553520-A-G

Variant names:

• chr5-168553520-A-G
• rs158898
• NM_024594.4:c.*4051T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024594.4. 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
	PANK3	NM_024594.4	MANE Select	c.*4051T>C		3_prime_UTR	Exon 7 of 7	NP_078870.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANK3	ENST00000239231.7	TSL:1 MANE Select	c.*4051T>C		3_prime_UTR	Exon 7 of 7	ENSP00000239231.6
	SLC2A3P1	ENST00000519666.1	TSL:6	n.208T>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.397 AC: 1962 AN: 4936

American (AMR) AF: 0.240 AC: 2695 AN: 11230

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1860 AN: 4212

East Asian (EAS) AF: 0.146 AC: 1144 AN: 7820

South Asian (SAS) AF: 0.470 AC: 17517 AN: 37308

European-Finnish (FIN) AF: 0.341 AC: 3098 AN: 9098

Middle Eastern (MID) AF: 0.435 AC: 288 AN: 662

European-Non Finnish (NFE) AF: 0.369 AC: 39348 AN: 106680

Other (OTH) AF: 0.367 AC: 3402 AN: 9258

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

African (AFR) AF: 0.403 AC: 16710 AN: 41458

American (AMR) AF: 0.276 AC: 4210 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1507 AN: 3472

East Asian (EAS) AF: 0.156 AC: 807 AN: 5184

South Asian (SAS) AF: 0.465 AC: 2245 AN: 4824

European-Finnish (FIN) AF: 0.360 AC: 3811 AN: 10588

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25262 AN: 67974

Other (OTH) AF: 0.375 AC: 789 AN: 2106

Alfa AF: 0.370 Hom.: 17835

Bravo AF: 0.355

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	6.0
DANN	Benign	0.84
PhyloP100		3.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs158898; hg19: chr5-167980525;