Genetic Variant PANK3:c.29-13_29-11dupTTT (chr5-168569008-G-GAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_024594.4(PANK3):c.29-13_29-11dupTTT 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 0.0025 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00024 ( 0 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.29-13_29-11dupTTT		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.29-11_29-10insTTT	intron	N/A	ENSP00000239231.6	Q9H999
PANK3	ENST00000908768.1		c.29-11_29-10insTTT	intron	N/A	ENSP00000578827.1
PANK3	ENST00000522176.1	TSL:5	c.-17-11_-17-10insTTT	intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes

AF:

0.00253

AC:

127

AN:

50138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000969

Gnomad AMI

AF:

0.00435

Gnomad AMR

AF:

0.00168

Gnomad ASJ

AF:

0.00263

Gnomad EAS

AF:

0.00316

Gnomad SAS

AF:

0.00331

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00335

Gnomad OTH

AF:

0.00179

GnomAD4 exome

AF:

0.000244

AC:

AN:

41008

Hom.:

Cov.:

AF XY:

0.000232

AC XY:

AN XY:

21598

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

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:

0.00

AC:

AN:

4128

South Asian (SAS)

AF:

0.00

AC:

AN:

912

European-Finnish (FIN)

AF:

0.000325

AC:

AN:

3080

Middle Eastern (MID)

AF:

0.00

AC:

AN:

242

European-Non Finnish (NFE)

AF:

0.000258

AC:

AN:

27140

Other (OTH)

AF:

0.000950

AC:

AN:

2106

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000000000000111022), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.285

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.00253

AC:

127

AN:

50160

Hom.:

Cov.:

AF XY:

0.00242

AC XY:

AN XY:

21510

show subpopulations

African (AFR)

AF:

0.000967

AC:

AN:

13442

American (AMR)

AF:

0.00167

AC:

AN:

2986

Ashkenazi Jewish (ASJ)

AF:

0.00263

AC:

AN:

1522

East Asian (EAS)

AF:

0.00316

AC:

AN:

948

South Asian (SAS)

AF:

0.00332

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:

0.00335

AC:

AN:

28614

Other (OTH)

AF:

0.00179

AC:

AN:

560

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.403

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

-1.4

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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-GAAAAAAAAAAAAAAAAAAA

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