Genetic Variant PALLD:p.Pro89Pro (chr4-168878158-G-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7

The NM_001166110.2(PALLD):c.267G>C(p.Pro89Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P89P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0014 ( 0 hom., cov: 32)

Exomes 𝑓: 0.012 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PALLD
NM_001166110.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.98

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 4-168878158-G-C is Benign according to our data. Variant chr4-168878158-G-C is described in ClinVar as Benign. ClinVar VariationId is 215804.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.98 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166110.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PALLD	NM_001166108.2	MANE Select	c.1965-12764G>C		intron	N/A	NP_001159580.1	Q8WX93-9
PALLD	NM_001166110.2		c.267G>C	p.Pro89Pro	synonymous	Exon 2 of 12	NP_001159582.1	Q8WX93-4
PALLD	NM_016081.4		c.1965-12764G>C		intron	N/A	NP_057165.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PALLD	ENST00000507735.6	TSL:1	c.267G>C	p.Pro89Pro	synonymous	Exon 2 of 12	ENSP00000424016.1	Q8WX93-4
PALLD	ENST00000505667.6	TSL:1 MANE Select	c.1965-12764G>C		intron	N/A	ENSP00000425556.1	Q8WX93-9
PALLD	ENST00000261509.10	TSL:1	c.1965-12764G>C		intron	N/A	ENSP00000261509.6	Q8WX93-2

Frequencies

GnomAD3 genomes

AF:

0.00142

AC:

183

AN:

129164

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00271

Gnomad AMI

AF:

0.00133

Gnomad AMR

AF:

0.000837

Gnomad ASJ

AF:

0.000311

Gnomad EAS

AF:

0.00179

Gnomad SAS

AF:

0.00308

Gnomad FIN

AF:

0.00403

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000441

Gnomad OTH

AF:

0.00168

GnomAD2 exomes

AF:

0.0161

AC:

1152

AN:

71534

AF XY:

0.0128

show subpopulations

Gnomad AFR exome

AF:

0.0627

Gnomad AMR exome

AF:

0.0513

Gnomad ASJ exome

AF:

0.0143

Gnomad EAS exome

AF:

0.0169

Gnomad FIN exome

AF:

0.00958

Gnomad NFE exome

AF:

0.00922

Gnomad OTH exome

AF:

0.0172

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0115

AC:

7237

AN:

629276

Hom.:

Cov.:

AF XY:

0.0107

AC XY:

3385

AN XY:

315000

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0217

AC:

243

AN:

11194

American (AMR)

AF:

0.0525

AC:

709

AN:

13508

Ashkenazi Jewish (ASJ)

AF:

0.0127

AC:

136

AN:

10668

East Asian (EAS)

AF:

0.00896

AC:

AN:

6138

South Asian (SAS)

AF:

0.00674

AC:

360

AN:

53404

European-Finnish (FIN)

AF:

0.00966

AC:

100

AN:

10356

Middle Eastern (MID)

AF:

0.0165

AC:

AN:

1756

European-Non Finnish (NFE)

AF:

0.0106

AC:

5295

AN:

498798

Other (OTH)

AF:

0.0132

AC:

310

AN:

23454

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.257

Heterozygous variant carriers

946

1891

2837

3782

4728

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

232

464

696

928

1160

<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

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00140

AC:

181

AN:

129240

Hom.:

Cov.:

AF XY:

0.00130

AC XY:

AN XY:

62876

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00271

AC:

AN:

33574

American (AMR)

AF:

0.000835

AC:

AN:

13174

Ashkenazi Jewish (ASJ)

AF:

0.000311

AC:

AN:

3218

East Asian (EAS)

AF:

0.00179

AC:

AN:

3910

South Asian (SAS)

AF:

0.00279

AC:

AN:

3582

European-Finnish (FIN)

AF:

0.00403

AC:

AN:

7690

Middle Eastern (MID)

AF:

0.00

AC:

AN:

266

European-Non Finnish (NFE)

AF:

0.000424

AC:

AN:

61264

Other (OTH)

AF:

0.00166

AC:

AN:

1808

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.255

Heterozygous variant carriers

116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.00816

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

not specified (1)

Pancreatic adenocarcinoma (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.87

(source)

DANN

Benign

0.59

PhyloP100

-3.0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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