5-168569008-GAAAAAAAAAAAAAAAA-GA

Variant names:

• chr5-168569008-GAAAAAAAAAAAAAAA-G
• rs368234880
• NM_024594.4:c.29-25_29-11delTTTTTTTTTTTTTTT

Variant summary

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

The NM_024594.4(PANK3):​c.29-25_29-11delTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000060 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00022 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: PANK3 NM_024594.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• 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.29-25_29-11delTTTTTTTTTTTTTTT		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.29-25_29-11delTTTTTTTTTTTTTTT		intron	N/A	ENSP00000239231.6	Q9H999
	PANK3	ENST00000908768.1		c.29-25_29-11delTTTTTTTTTTTTTTT		intron	N/A	ENSP00000578827.1
	PANK3	ENST00000522176.1	TSL:5	c.-17-25_-17-11delTTTTTTTTTTTTTTT		intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes AF: 0.0000597 AC: 3 AN: 50212 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00221

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00179

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000219 AC: 9 AN: 41026 Hom.: 1 AF XY: 0.000278 AC XY: 6 AN XY: 21612

African (AFR) AF: 0.00 AC: 0 AN: 810

American (AMR) AF: 0.00 AC: 0 AN: 1524

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

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

South Asian (SAS) AF: 0.00768 AC: 7 AN: 912

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3082

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

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 27156

Other (OTH) AF: 0.000950 AC: 2 AN: 2106

GnomAD4 genome AF: 0.0000597 AC: 3 AN: 50234 Hom.: 0 Cov.: 0 AF XY: 0.000139 AC XY: 3 AN XY: 21548

African (AFR) AF: 0.00 AC: 0 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: 0.00221 AC: 2 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: 0.00179 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		1.1

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;