5-168569008-G-GA

Position:

• chr5-168569008-G-GA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_024594.4(PANK3):​c.29-11_29-10insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (1188 hom., cov: 0)
  • Exomes 𝑓: 0.026 (0 hom.)
• Consequence: PANK3 NM_024594.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.35

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-168569008-G-GA is Benign according to our data. Variant chr5-168569008-G-GA is described in ClinVar as [Benign]. Clinvar id is 2776131.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PANK3	NM_024594.4	c.29-11_29-10insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000239231.7	NP_078870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PANK3	ENST00000239231.7	c.29-11_29-10insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_024594.4	ENSP00000239231	P1
PANK3	ENST00000522176.1	c.-17-11_-17-10insT		splice_polypyrimidine_tract_variant, intron_variant		5		ENSP00000428631

Frequencies

GnomAD3 genomes AF: 0.166 AC: 8313 AN: 50082 Hom.: 1190 Cov.: 0

Gnomad AFR AF: 0.0794

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.0796

Gnomad MID AF: 0.106

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.185

GnomAD3 exomes AF: 0.00307 AC: 16 AN: 5208 Hom.: 0 AF XY: 0.00190 AC XY: 5 AN XY: 2632

Gnomad AFR exome AF: 0.00833

Gnomad AMR exome AF: 0.00275

Gnomad ASJ exome AF: 0.0204

Gnomad EAS exome AF: 0.00256

Gnomad SAS exome AF: 0.00307

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00253

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0263 AC: 1075 AN: 40838 Hom.: 0 Cov.: 1 AF XY: 0.0277 AC XY: 595 AN XY: 21498

Gnomad4 AFR exome AF: 0.00995

Gnomad4 AMR exome AF: 0.00594

Gnomad4 ASJ exome AF: 0.0216

Gnomad4 EAS exome AF: 0.00243

Gnomad4 SAS exome AF: 0.0233

Gnomad4 FIN exome AF: 0.00618

Gnomad4 NFE exome AF: 0.0348

Gnomad4 OTH exome AF: 0.0190

GnomAD4 genome AF: 0.166 AC: 8310 AN: 50104 Hom.: 1188 Cov.: 0 AF XY: 0.159 AC XY: 3410 AN XY: 21486

Gnomad4 AFR AF: 0.0794

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0406

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.0796

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.185

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 15, 2023

- -

Computational scores

Source: dbNSFP v4.3

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: rs368234880; hg19: chr5-167996013;