5-168569008-GAAAAAAAAAAAAAAAA-GAAAAA

Variant names:

• chr5-168569008-GAAAAAAAAAAA-G
• rs368234880
• NM_024594.4:c.29-21_29-11delTTTTTTTTTTT

Variant summary

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

The NM_024594.4(PANK3):​c.29-21_29-11delTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 91,236 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000020 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000049 (0 hom.)
• Consequence: PANK3 NM_024594.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.25
• 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.29-21_29-11delTTTTTTTTTTT		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.29-21_29-11delTTTTTTTTTTT		intron	N/A	ENSP00000239231.6	Q9H999
	PANK3	ENST00000908768.1		c.29-21_29-11delTTTTTTTTTTT		intron	N/A	ENSP00000578827.1
	PANK3	ENST00000522176.1	TSL:5	c.-17-21_-17-11delTTTTTTTTTTT		intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes AF: 0.0000199 AC: 1 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: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000349

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000488 AC: 2 AN: 41024 Hom.: 0 AF XY: 0.0000925 AC XY: 2 AN XY: 21610

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: 0.00 AC: 0 AN: 912

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3080

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

European-Non Finnish (NFE) AF: 0.0000736 AC: 2 AN: 27156

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

GnomAD4 genome AF: 0.0000199 AC: 1 AN: 50212 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 21524

African (AFR) AF: 0.00 AC: 0 AN: 13418

American (AMR) AF: 0.00 AC: 0 AN: 2986

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 950

South Asian (SAS) AF: 0.00 AC: 0 AN: 906

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 66

European-Non Finnish (NFE) AF: 0.0000349 AC: 1 AN: 28676

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		3.2
Mutation Taster		=100/0	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;