5-168569008-GAAAAAAAAAAAAAAAA-GAAAAAAAA

Variant names:

• chr5-168569008-GAAAAAAAA-G
• rs368234880
• NM_024594.4:c.29-18_29-11delTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_024594.4(PANK3):​c.29-18_29-11delTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00156 in 91,250 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0021 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00085 (0 hom.)
• Consequence: PANK3 NM_024594.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772
• Publications: 0 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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANK3	NM_024594.4	MANE Select	c.29-18_29-11delTTTTTTTT		intron	N/A	NP_078870.1	Q9H999

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PANK3	ENST00000239231.7	TSL:1 MANE Select	c.29-18_29-11delTTTTTTTT		intron	N/A	ENSP00000239231.6	Q9H999
	PANK3	ENST00000908768.1		c.29-18_29-11delTTTTTTTT		intron	N/A	ENSP00000578827.1
	PANK3	ENST00000522176.1	TSL:5	c.-17-18_-17-11delTTTTTTTT		intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes AF: 0.00213 AC: 107 AN: 50216 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00745

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000670

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000105

Gnomad OTH AF: 0.00179

GnomAD4 exome AF: 0.000853 AC: 35 AN: 41012 Hom.: 0 AF XY: 0.000787 AC XY: 17 AN XY: 21602

African (AFR) AF: 0.0185 AC: 15 AN: 810

American (AMR) AF: 0.00131 AC: 2 AN: 1522

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1064

East Asian (EAS) AF: 0.00 AC: 0 AN: 4128

South Asian (SAS) AF: 0.00 AC: 0 AN: 912

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3078

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 242

European-Non Finnish (NFE) AF: 0.000331 AC: 9 AN: 27152

Other (OTH) AF: 0.00428 AC: 9 AN: 2104

GnomAD4 genome AF: 0.00213 AC: 107 AN: 50238 Hom.: 0 Cov.: 0 AF XY: 0.00223 AC XY: 48 AN XY: 21550

African (AFR) AF: 0.00743 AC: 100 AN: 13450

American (AMR) AF: 0.000669 AC: 2 AN: 2988

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1528

East Asian (EAS) AF: 0.00 AC: 0 AN: 948

South Asian (SAS) AF: 0.00 AC: 0 AN: 904

European-Finnish (FIN) AF: 0.00151 AC: 1 AN: 662

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 64

European-Non Finnish (NFE) AF: 0.000105 AC: 3 AN: 28674

Other (OTH) AF: 0.00179 AC: 1 AN: 560

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.77
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs368234880; hg19: chr5-167996013;