Genetic Variant NM_024594.4:c.*4051T>C (chr5-168553520-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024594.4(PANK3):c.*4051T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 343,292 control chromosomes in the GnomAD database, including 24,590 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 10408 hom., cov: 32)

Exomes 𝑓: 0.37 ( 14182 hom. )

Consequence

PANK3
NM_024594.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.49

Publications

4 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:

SLC2A3P1 (HGNC:11008): (solute carrier family 2 member 3 pseudogene 1)

SLC2A3P1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PANK3	NM_024594.4 link	c.*4051T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000239231.7	NP_078870.1
SLC2A3P1		n.168553520A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PANK3	ENST00000239231.7 link	c.*4051T>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_024594.4	ENSP00000239231.6
SLC2A3P1	ENST00000519666.1 link	n.208T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.367

AC:

55707

AN:

151970

Hom.:

10396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.403

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.276

Gnomad ASJ

AF:

0.434

Gnomad EAS

AF:

0.156

Gnomad SAS

AF:

0.464

Gnomad FIN

AF:

0.360

Gnomad MID

AF:

0.405

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.378

GnomAD4 exome

AF:

0.373

AC:

71314

AN:

191204

Hom.:

14182

Cov.:

AF XY:

0.382

AC XY:

40567

AN XY:

106066

show subpopulations

African (AFR)

AF:

0.397

AC:

1962

AN:

4936

American (AMR)

AF:

0.240

AC:

2695

AN:

11230

Ashkenazi Jewish (ASJ)

AF:

0.442

AC:

1860

AN:

4212

East Asian (EAS)

AF:

0.146

AC:

1144

AN:

7820

South Asian (SAS)

AF:

0.470

AC:

17517

AN:

37308

European-Finnish (FIN)

AF:

0.341

AC:

3098

AN:

9098

Middle Eastern (MID)

AF:

0.435

AC:

288

AN:

662

European-Non Finnish (NFE)

AF:

0.369

AC:

39348

AN:

106680

Other (OTH)

AF:

0.367

AC:

3402

AN:

9258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1939

3877

5816

7754

9693

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.367

AC:

55743

AN:

152088

Hom.:

10408

Cov.:

AF XY:

0.362

AC XY:

26924

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.403

AC:

16710

AN:

41458

American (AMR)

AF:

0.276

AC:

4210

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.434

AC:

1507

AN:

3472

East Asian (EAS)

AF:

0.156

AC:

807

AN:

5184

South Asian (SAS)

AF:

0.465

AC:

2245

AN:

4824

European-Finnish (FIN)

AF:

0.360

AC:

3811

AN:

10588

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.372

AC:

25262

AN:

67974

Other (OTH)

AF:

0.375

AC:

789

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1817

3634

5451

7268

9085

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

542

1084

1626

2168

2710

<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:

0.370

Hom.:

17835

Bravo

AF:

0.355

Asia WGS

AF:

0.308

AC:

1072

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

6.0

(source)

DANN

Benign

0.84

PhyloP100

3.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over