Genetic Variant PALLD:n.3748dupA (chr4-168928326-T-TA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000507699.1(PALLD):n.3748dupA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.070 ( 577 hom., cov: 0)

Exomes 𝑓: 0.042 ( 12 hom. )

Consequence

PALLD
ENST00000507699.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 3.04

Publications

1 publications found

Variant links:

Genes affected

PALLD (HGNC:17068): (palladin, cytoskeletal associated protein) This gene encodes a cytoskeletal protein that is required for organizing the actin cytoskeleton. The protein is a component of actin-containing microfilaments, and it is involved in the control of cell shape, adhesion, and contraction. Polymorphisms in this gene are associated with a susceptibility to pancreatic cancer type 1, and also with a risk for myocardial infarction. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

PALLD links:

CBR4 (HGNC:25891): (carbonyl reductase 4) Enables several functions, including 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity; NADPH binding activity; and NADPH dehydrogenase (quinone) activity. Involved in fatty acid biosynthetic process; glycoside metabolic process; and protein tetramerization. Located in mitochondrial matrix. Part of oxidoreductase complex. [provided by Alliance of Genome Resources, Apr 2022]

CBR4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALLD	NM_001166108.2 link	c.*2156dupA		3_prime_UTR_variant	Exon 22 of 22	ENST00000505667.6	NP_001159580.1	Q8WX93-9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALLD	ENST00000505667.6 link	c.*2156dupA		3_prime_UTR_variant	Exon 22 of 22	1	NM_001166108.2	ENSP00000425556.1		Q8WX93-9

Frequencies

GnomAD3 genomes

AF:

0.0698

AC:

10563

AN:

151314

Hom.:

576

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.0615

Gnomad AMR

AF:

0.0518

Gnomad ASJ

AF:

0.0732

Gnomad EAS

AF:

0.00136

Gnomad SAS

AF:

0.00934

Gnomad FIN

AF:

0.00888

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0399

Gnomad OTH

AF:

0.0692

GnomAD4 exome

AF:

0.0423

AC:

1183

AN:

27994

Hom.:

Cov.:

AF XY:

0.0416

AC XY:

535

AN XY:

12850

show subpopulations

African (AFR)

AF:

0.133

AC:

127

AN:

958

American (AMR)

AF:

0.0410

AC:

AN:

610

Ashkenazi Jewish (ASJ)

AF:

0.0685

AC:

121

AN:

1766

East Asian (EAS)

AF:

0.00109

AC:

AN:

5512

South Asian (SAS)

AF:

0.00

AC:

AN:

228

European-Finnish (FIN)

AF:

0.00905

AC:

AN:

442

Middle Eastern (MID)

AF:

0.0930

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.0459

AC:

735

AN:

16012

Other (OTH)

AF:

0.0650

AC:

149

AN:

2294

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.452

Heterozygous variant carriers

133

178

222

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:

0.0699

AC:

10580

AN:

151428

Hom.:

577

Cov.:

AF XY:

0.0658

AC XY:

4871

AN XY:

73996

show subpopulations

African (AFR)

AF:

0.157

AC:

6465

AN:

41072

American (AMR)

AF:

0.0517

AC:

787

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.0732

AC:

254

AN:

3470

East Asian (EAS)

AF:

0.00136

AC:

AN:

5150

South Asian (SAS)

AF:

0.00935

AC:

AN:

4812

European-Finnish (FIN)

AF:

0.00888

AC:

AN:

10476

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0399

AC:

2709

AN:

67912

Other (OTH)

AF:

0.0685

AC:

144

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

456

912

1369

1825

2281

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0114

Hom.:

1399

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Carcinoma of pancreas

Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Uncertain:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.0

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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4-168928326-TAAAA-TAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over