Genetic Variant PANK3:c.29-13_29-11delTTT (chr5-168569008-GAAA-G) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The NM_024594.4(PANK3):c.29-13_29-11delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0128 in 90,862 control chromosomes in the GnomAD database, including 38 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0095 ( 3 hom., cov: 0)

Exomes 𝑓: 0.017 ( 35 hom. )

Consequence

PANK3
NM_024594.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.676

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.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00954 (479/50186) while in subpopulation AFR AF = 0.033 (443/13410). AF 95% confidence interval is 0.0305. There are 3 homozygotes in GnomAd4. There are 222 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 3 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.29-13_29-11delTTT		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.29-13_29-11delTTT	intron	N/A	ENSP00000239231.6	Q9H999
PANK3	ENST00000908768.1		c.29-13_29-11delTTT	intron	N/A	ENSP00000578827.1
PANK3	ENST00000522176.1	TSL:5	c.-17-13_-17-11delTTT	intron	N/A	ENSP00000428631.1	E5RHA5

Frequencies

GnomAD3 genomes

AF:

0.00953

AC:

478

AN:

50164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0330

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00772

Gnomad ASJ

AF:

0.000654

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00110

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000174

Gnomad OTH

AF:

0.0108

GnomAD2 exomes

AF:

0.0515

AC:

268

AN:

5208

AF XY:

0.0578

show subpopulations

Gnomad AFR exome

AF:

0.0333

Gnomad AMR exome

AF:

0.0412

Gnomad ASJ exome

AF:

0.0816

Gnomad EAS exome

AF:

0.0359

Gnomad FIN exome

AF:

0.0373

Gnomad NFE exome

AF:

0.0574

Gnomad OTH exome

AF:

0.0714

GnomAD4 exome

AF:

0.0168

AC:

683

AN:

40676

Hom.:

AF XY:

0.0185

AC XY:

396

AN XY:

21406

show subpopulations

African (AFR)

AF:

0.0214

AC:

AN:

794

American (AMR)

AF:

0.0252

AC:

AN:

1510

Ashkenazi Jewish (ASJ)

AF:

0.0265

AC:

AN:

1056

East Asian (EAS)

AF:

0.00219

AC:

AN:

4110

South Asian (SAS)

AF:

0.0363

AC:

AN:

910

European-Finnish (FIN)

AF:

0.0186

AC:

AN:

3068

Middle Eastern (MID)

AF:

0.00833

AC:

AN:

240

European-Non Finnish (NFE)

AF:

0.0171

AC:

461

AN:

26904

Other (OTH)

AF:

0.0182

AC:

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.402

Heterozygous variant carriers

131

164

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:

0.00954

AC:

479

AN:

50186

Hom.:

Cov.:

AF XY:

0.0103

AC XY:

222

AN XY:

21520

show subpopulations

African (AFR)

AF:

0.0330

AC:

443

AN:

13410

American (AMR)

AF:

0.00771

AC:

AN:

2982

Ashkenazi Jewish (ASJ)

AF:

0.000654

AC:

AN:

1528

East Asian (EAS)

AF:

0.00

AC:

AN:

948

South Asian (SAS)

AF:

0.00111

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:

0.000174

AC:

AN:

28672

Other (OTH)

AF:

0.0108

AC:

AN:

558

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.456

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

0.68

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

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5-168569008-GAAAAAAAAAAAAAAAA-GAAAAAAAAAAAAA

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