5-168569008-GAAAAAAAAAAAAAAAA-GAAAAAAAAA

Variant names:

• chr5-168569008-GAAAAAAA-G
• rs368234880
• NM_024594.4:c.29-17_29-11delTTTTTTT

Variant summary

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

The NM_024594.4(PANK3):​c.29-17_29-11delTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0008 in 91,234 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00036 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0013 (1 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.29-17_29-11delTTTTTTT		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.29-17_29-11delTTTTTTT		intron	N/A	ENSP00000239231.6	Q9H999
	PANK3	ENST00000908768.1		c.29-17_29-11delTTTTTTT		intron	N/A	ENSP00000578827.1
	PANK3	ENST00000522176.1	TSL:5	c.-17-17_-17-11delTTTTTTT		intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes AF: 0.000358 AC: 18 AN: 50212 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000745

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000654

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00110

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000209

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00134 AC: 55 AN: 41000 Hom.: 1 AF XY: 0.00157 AC XY: 34 AN XY: 21594

African (AFR) AF: 0.00743 AC: 6 AN: 808

American (AMR) AF: 0.00262 AC: 4 AN: 1524

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1066

East Asian (EAS) AF: 0.000242 AC: 1 AN: 4128

South Asian (SAS) AF: 0.00549 AC: 5 AN: 910

European-Finnish (FIN) AF: 0.000649 AC: 2 AN: 3080

Middle Eastern (MID) AF: 0.00413 AC: 1 AN: 242

European-Non Finnish (NFE) AF: 0.00118 AC: 32 AN: 27136

Other (OTH) AF: 0.00190 AC: 4 AN: 2106

GnomAD4 genome AF: 0.000358 AC: 18 AN: 50234 Hom.: 0 Cov.: 0 AF XY: 0.000371 AC XY: 8 AN XY: 21548

African (AFR) AF: 0.000744 AC: 10 AN: 13446

American (AMR) AF: 0.00 AC: 0 AN: 2988

Ashkenazi Jewish (ASJ) AF: 0.000654 AC: 1 AN: 1528

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

South Asian (SAS) AF: 0.00111 AC: 1 AN: 904

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 662

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

European-Non Finnish (NFE) AF: 0.000209 AC: 6 AN: 28674

Other (OTH) AF: 0.00 AC: 0 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

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;