Genetic Variant PALLD:n.3748delA (chr4-168928326-TA-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Frequency

Genomes: 𝑓 0.67 ( 35550 hom., cov: 0)

Exomes 𝑓: 0.76 ( 8176 hom. )

Consequence

PALLD
ENST00000507699.1 non_coding_transcript_exon

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

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 -10 ACMG points.

BP6

Variant 4-168928326-TA-T is Benign according to our data. Variant chr4-168928326-TA-T is described in ClinVar as Benign. ClinVar VariationId is 348072.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

AF:

0.669

AC:

101266

AN:

151282

Hom.:

35539

Cov.:

show subpopulations

Gnomad AFR

AF:

0.439

Gnomad AMI

AF:

0.812

Gnomad AMR

AF:

0.703

Gnomad ASJ

AF:

0.694

Gnomad EAS

AF:

0.954

Gnomad SAS

AF:

0.787

Gnomad FIN

AF:

0.803

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.746

Gnomad OTH

AF:

0.683

GnomAD4 exome

AF:

0.760

AC:

21290

AN:

27996

Hom.:

8176

Cov.:

AF XY:

0.766

AC XY:

9837

AN XY:

12844

show subpopulations

African (AFR)

AF:

0.465

AC:

443

AN:

952

American (AMR)

AF:

0.726

AC:

446

AN:

614

Ashkenazi Jewish (ASJ)

AF:

0.703

AC:

1248

AN:

1776

East Asian (EAS)

AF:

0.942

AC:

5192

AN:

5512

South Asian (SAS)

AF:

0.781

AC:

175

AN:

224

European-Finnish (FIN)

AF:

0.794

AC:

351

AN:

442

Middle Eastern (MID)

AF:

0.709

AC:

122

AN:

172

European-Non Finnish (NFE)

AF:

0.733

AC:

11730

AN:

16012

Other (OTH)

AF:

0.691

AC:

1583

AN:

2292

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

233

466

698

931

1164

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

136

204

272

340

<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:

0.669

AC:

101316

AN:

151396

Hom.:

35550

Cov.:

AF XY:

0.676

AC XY:

50011

AN XY:

73982

show subpopulations

African (AFR)

AF:

0.438

AC:

17990

AN:

41048

American (AMR)

AF:

0.704

AC:

10712

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.694

AC:

2407

AN:

3470

East Asian (EAS)

AF:

0.954

AC:

4917

AN:

5152

South Asian (SAS)

AF:

0.788

AC:

3790

AN:

4810

European-Finnish (FIN)

AF:

0.803

AC:

8407

AN:

10472

Middle Eastern (MID)

AF:

0.755

AC:

222

AN:

294

European-Non Finnish (NFE)

AF:

0.746

AC:

50688

AN:

67912

Other (OTH)

AF:

0.686

AC:

1444

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1542

3084

4625

6167

7709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

804

1608

2412

3216

4020

<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:

0.660

Hom.:

1399

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Carcinoma of pancreas

Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

3.0

Mutation Taster

=99/1

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-TAAA

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