Genetic Variant PANK3:c.29-11delT (chr5-168569008-GA-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.29-11delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.067 ( 98 hom., cov: 0)

Exomes 𝑓: 0.045 ( 76 hom. )

Consequence

PANK3
NM_024594.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35

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 (AFR) allele frequency at 95% confidence interval = 0.127 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.29-11delT		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.29-11delT	intron	N/A	ENSP00000239231.6	Q9H999
PANK3	ENST00000908768.1		c.29-11delT	intron	N/A	ENSP00000578827.1
PANK3	ENST00000522176.1	TSL:5	c.-17-11delT	intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes

AF:

0.0671

AC:

3349

AN:

49880

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.132

Gnomad AMI

AF:

0.0830

Gnomad AMR

AF:

0.0400

Gnomad ASJ

AF:

0.0335

Gnomad EAS

AF:

0.00316

Gnomad SAS

AF:

0.0122

Gnomad FIN

AF:

0.0468

Gnomad MID

AF:

0.0909

Gnomad NFE

AF:

0.0464

Gnomad OTH

AF:

0.0489

GnomAD2 exomes

AF:

0.0591

AC:

308

AN:

5208

AF XY:

0.0631

show subpopulations

Gnomad AFR exome

AF:

0.0292

Gnomad AMR exome

AF:

0.0714

Gnomad ASJ exome

AF:

0.0204

Gnomad EAS exome

AF:

0.0846

Gnomad FIN exome

AF:

0.0254

Gnomad NFE exome

AF:

0.0690

Gnomad OTH exome

AF:

0.0804

GnomAD4 exome

AF:

0.0448

AC:

1831

AN:

40828

Hom.:

Cov.:

AF XY:

0.0449

AC XY:

965

AN XY:

21500

show subpopulations

African (AFR)

AF:

0.0537

AC:

AN:

800

American (AMR)

AF:

0.0409

AC:

AN:

1516

Ashkenazi Jewish (ASJ)

AF:

0.0235

AC:

AN:

1066

East Asian (EAS)

AF:

0.00900

AC:

AN:

4112

South Asian (SAS)

AF:

0.0496

AC:

AN:

908

European-Finnish (FIN)

AF:

0.0287

AC:

AN:

3062

Middle Eastern (MID)

AF:

0.0375

AC:

AN:

240

European-Non Finnish (NFE)

AF:

0.0535

AC:

1446

AN:

27028

Other (OTH)

AF:

0.0363

AC:

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.420

Heterozygous variant carriers

168

253

337

421

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

108

144

180

<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:

0.0672

AC:

3355

AN:

49902

Hom.:

Cov.:

AF XY:

0.0676

AC XY:

1447

AN XY:

21414

show subpopulations

African (AFR)

AF:

0.132

AC:

1740

AN:

13202

American (AMR)

AF:

0.0403

AC:

120

AN:

2974

Ashkenazi Jewish (ASJ)

AF:

0.0335

AC:

AN:

1524

East Asian (EAS)

AF:

0.00316

AC:

AN:

948

South Asian (SAS)

AF:

0.0122

AC:

AN:

902

European-Finnish (FIN)

AF:

0.0468

AC:

AN:

662

Middle Eastern (MID)

AF:

0.0938

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0464

AC:

1327

AN:

28616

Other (OTH)

AF:

0.0507

AC:

AN:

552

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.426

Heterozygous variant carriers

118

235

353

470

588

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

108

144

180

<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

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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5-168569008-GAAAAAAAAAAAAAAAA-GAAAAAAAAAAAAAAA

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