chr5-168569008-GAAAAAAAAA-G

Variant names:

• chr5-168569008-GAAAAAAAAA-G
• rs368234880
• NM_024594.4:c.29-19_29-11delTTTTTTTTT

Variant summary

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

The NM_024594.4(PANK3):​c.29-19_29-11delTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000647 in 91,258 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 0.00068 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00061 (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.29-19_29-11delTTTTTTTTT		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.29-19_29-11delTTTTTTTTT		intron	N/A	ENSP00000239231.6	Q9H999
	PANK3	ENST00000908768.1		c.29-19_29-11delTTTTTTTTT		intron	N/A	ENSP00000578827.1
	PANK3	ENST00000522176.1	TSL:5	c.-17-19_-17-11delTTTTTTTTT		intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes AF: 0.000677 AC: 34 AN: 50212 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00253

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000609 AC: 25 AN: 41024 Hom.: 0 AF XY: 0.000324 AC XY: 7 AN XY: 21610

African (AFR) AF: 0.0111 AC: 9 AN: 810

American (AMR) AF: 0.00263 AC: 4 AN: 1522

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

East Asian (EAS) AF: 0.000484 AC: 2 AN: 4128

South Asian (SAS) AF: 0.00219 AC: 2 AN: 912

European-Finnish (FIN) AF: 0.000649 AC: 2 AN: 3082

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

European-Non Finnish (NFE) AF: 0.000221 AC: 6 AN: 27156

Other (OTH) AF: 0.00 AC: 0 AN: 2106

GnomAD4 genome AF: 0.000677 AC: 34 AN: 50234 Hom.: 0 Cov.: 0 AF XY: 0.000696 AC XY: 15 AN XY: 21548

African (AFR) AF: 0.00253 AC: 34 AN: 13446

American (AMR) AF: 0.00 AC: 0 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: 0.00 AC: 0 AN: 662

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

European-Non Finnish (NFE) AF: 0.00 AC: 0 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;