Genetic Variant PANK3:c.29-14_29-11delTTTT (chr5-168569008-GAAAA-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_024594.4(PANK3):c.29-14_29-11delTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00417 in 91,028 control chromosomes in the GnomAD database, including 13 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00038 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0088 ( 13 hom. )

Consequence

PANK3
NM_024594.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.764

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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 13 AR gene

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.29-14_29-11delTTTT		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.29-14_29-11delTTTT	intron	N/A	ENSP00000239231.6	Q9H999
PANK3	ENST00000908768.1		c.29-14_29-11delTTTT	intron	N/A	ENSP00000578827.1
PANK3	ENST00000522176.1	TSL:5	c.-17-14_-17-11delTTTT	intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes

AF:

0.000378

AC:

AN:

50204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00127

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000335

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

GnomAD2 exomes

AF:

0.0405

AC:

211

AN:

5208

AF XY:

0.0433

show subpopulations

Gnomad AFR exome

AF:

0.0146

Gnomad AMR exome

AF:

0.0549

Gnomad ASJ exome

AF:

0.0714

Gnomad EAS exome

AF:

0.0231

Gnomad FIN exome

AF:

0.0254

Gnomad NFE exome

AF:

0.0466

Gnomad OTH exome

AF:

0.0893

GnomAD4 exome

AF:

0.00885

AC:

361

AN:

40802

Hom.:

AF XY:

0.00954

AC XY:

205

AN XY:

21480

show subpopulations

African (AFR)

AF:

0.00995

AC:

AN:

804

American (AMR)

AF:

0.0166

AC:

AN:

1510

Ashkenazi Jewish (ASJ)

AF:

0.0113

AC:

AN:

1066

East Asian (EAS)

AF:

0.00364

AC:

AN:

4124

South Asian (SAS)

AF:

0.0221

AC:

AN:

906

European-Finnish (FIN)

AF:

0.0115

AC:

AN:

3052

Middle Eastern (MID)

AF:

0.00413

AC:

AN:

242

European-Non Finnish (NFE)

AF:

0.00848

AC:

229

AN:

27002

Other (OTH)

AF:

0.00763

AC:

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.421

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:

0.000378

AC:

AN:

50226

Hom.:

Cov.:

AF XY:

0.000511

AC XY:

AN XY:

21542

show subpopulations

African (AFR)

AF:

0.00127

AC:

AN:

13436

American (AMR)

AF:

0.000334

AC:

AN:

2990

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1528

East Asian (EAS)

AF:

0.00

AC:

AN:

948

South Asian (SAS)

AF:

0.00

AC:

AN:

904

European-Finnish (FIN)

AF:

0.00

AC:

AN:

662

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0000349

AC:

AN:

28674

Other (OTH)

AF:

0.00

AC:

AN:

560

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.459

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

0.76

Mutation Taster

=100/0

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

5-168569008-GAAAAAAAAAAAAAAAA-GAAAAAAAAAAAA

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