dbSNP rs3824603: PANK1:c.*556C>T (chr10-89583850-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_148977.3(PANK1):c.*556C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,376 control chromosomes in the GnomAD database, including 4,924 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 0.24 ( 4908 hom., cov: 32)

Exomes 𝑓: 0.28 ( 16 hom. )

Consequence

PANK1
NM_148977.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.271

Publications

6 publications found

Variant links:

Genes affected

PANK1 (HGNC:8598): (pantothenate kinase 1) This gene encodes a member of the pantothenate kinase family. Pantothenate kinases are key regulatory enzymes in the biosynthesis of coenzyme A (CoA). The encoded protein catalyzes the first and rate-limiting enzymatic reaction in CoA biosynthesis and is regulated by CoA through feedback inhibition. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. This gene and an intronic miRNA on the same strand are co-regulated by the tumor suppressor p53 (see PMID 20833636). [provided by RefSeq, Apr 2011]

PANK1 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_148977.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PANK1	NM_148977.3	MANE Select	c.*556C>T	3_prime_UTR	Exon 7 of 7	NP_683878.2	A0A8C8KBT8
PANK1	NM_148978.3		c.*556C>T	3_prime_UTR	Exon 7 of 7	NP_683879.1	Q8TE04-2
PANK1	NM_138316.4		c.*556C>T	3_prime_UTR	Exon 6 of 6	NP_612189.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PANK1	ENST00000307534.10	TSL:1 MANE Select	c.*556C>T	3_prime_UTR	Exon 7 of 7	ENSP00000302108.5	A0A8C8KBT8
PANK1	ENST00000342512.4	TSL:1	c.*556C>T	3_prime_UTR	Exon 7 of 7	ENSP00000345118.3	Q8TE04-2
PANK1	ENST00000322191.10	TSL:1	c.*556C>T	3_prime_UTR	Exon 6 of 6	ENSP00000318526.6	Q8TE04-3

Frequencies

GnomAD3 genomes

AF:

0.243

AC:

36891

AN:

151844

Hom.:

4900

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.165

Gnomad AMR

AF:

0.279

Gnomad ASJ

AF:

0.228

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.291

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.235

GnomAD4 exome

AF:

0.280

AC:

116

AN:

414

Hom.:

Cov.:

AF XY:

0.288

AC XY:

AN XY:

250

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.375

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.667

AC:

AN:

South Asian (SAS)

AF:

0.333

AC:

AN:

European-Finnish (FIN)

AF:

0.252

AC:

AN:

270

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.321

AC:

AN:

106

Other (OTH)

AF:

0.300

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

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:

0.243

AC:

36904

AN:

151962

Hom.:

4908

Cov.:

AF XY:

0.247

AC XY:

18361

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.137

AC:

5689

AN:

41472

American (AMR)

AF:

0.280

AC:

4270

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

791

AN:

3468

East Asian (EAS)

AF:

0.463

AC:

2391

AN:

5166

South Asian (SAS)

AF:

0.290

AC:

1396

AN:

4812

European-Finnish (FIN)

AF:

0.290

AC:

3061

AN:

10538

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.274

AC:

18607

AN:

67936

Other (OTH)

AF:

0.232

AC:

489

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1391

2782

4172

5563

6954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

398

796

1194

1592

1990

<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:

0.265

Hom.:

2261

Bravo

AF:

0.238

Asia WGS

AF:

0.368

AC:

1281

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.5

(source)

DANN

Benign

0.60

PhyloP100

0.27

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over