Genetic Variant PANK3:c.29-26_29-11delTTTTTTTTTTTTTTTT (chr5-168569008-GAAAAAAAAAAAAAAAA-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024594.4(PANK3):c.29-26_29-11delTTTTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00506 in 91,260 control chromosomes in the GnomAD database, including 58 homozygotes. 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. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.0018 ( 1 hom., cov: 0)

Exomes 𝑓: 0.0091 ( 57 hom. )

Consequence

PANK3
NM_024594.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.06

Publications

0 publications found

Variant links:

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]

PANK3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0741 is higher than 0.05.

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.29-26_29-11delTTTTTTTTTTTTTTTT		intron	N/A	NP_078870.1	Q9H999

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PANK3	ENST00000239231.7	TSL:1 MANE Select	c.29-26_29-11delTTTTTTTTTTTTTTTT	intron	N/A	ENSP00000239231.6	Q9H999
PANK3	ENST00000908768.1		c.29-26_29-11delTTTTTTTTTTTTTTTT	intron	N/A	ENSP00000578827.1
PANK3	ENST00000522176.1	TSL:5	c.-17-26_-17-11delTTTTTTTTTTTTTTTT	intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes

AF:

0.00177

AC:

AN:

50214

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000335

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0893

Gnomad SAS

AF:

0.00221

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00909

AC:

373

AN:

41024

Hom.:

AF XY:

0.00856

AC XY:

185

AN XY:

21610

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

810

American (AMR)

AF:

0.00

AC:

AN:

1524

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1066

East Asian (EAS)

AF:

0.0843

AC:

348

AN:

4126

South Asian (SAS)

AF:

0.0143

AC:

AN:

912

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3082

Middle Eastern (MID)

AF:

0.00413

AC:

AN:

242

European-Non Finnish (NFE)

AF:

0.0000368

AC:

AN:

27156

Other (OTH)

AF:

0.00475

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.665

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00177

AC:

AN:

50236

Hom.:

Cov.:

AF XY:

0.00241

AC XY:

AN XY:

21550

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13446

American (AMR)

AF:

0.000335

AC:

AN:

2988

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1528

East Asian (EAS)

AF:

0.0895

AC:

AN:

950

South Asian (SAS)

AF:

0.00221

AC:

AN:

904

European-Finnish (FIN)

AF:

0.00151

AC:

AN:

662

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

28674

Other (OTH)

AF:

0.00

AC:

AN:

560

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.629

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over