Genetic Variant PALLD:c.1964+44412G>A (chr4-168756335-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_001166108.2(PALLD):c.1964+44412G>A variant causes a intron change. The variant allele was found at a frequency of 0.417 in 223,958 control chromosomes in the GnomAD database, including 23,643 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 0.44 ( 17938 hom., cov: 32)

Exomes 𝑓: 0.37 ( 5705 hom. )

Consequence

PALLD
NM_001166108.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.62

Publications

9 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:

RPL9P16 (HGNC:36851): (ribosomal protein L9 pseudogene 16)

RPL9P16 links:

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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=-0.67).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALLD	NM_001166108.2 link	c.1964+44412G>A		intron_variant	Intron 10 of 21	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.1964+44412G>A		intron_variant	Intron 10 of 21	1	NM_001166108.2	ENSP00000425556.1		Q8WX93-9

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66538

AN:

151944

Hom.:

17944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.130

Gnomad SAS

AF:

0.429

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.618

Gnomad OTH

AF:

0.445

GnomAD4 exome

AF:

0.374

AC:

26885

AN:

71896

Hom.:

5705

Cov.:

AF XY:

0.371

AC XY:

15426

AN XY:

41614

show subpopulations

African (AFR)

AF:

0.0832

AC:

160

AN:

1922

American (AMR)

AF:

0.151

AC:

1103

AN:

7304

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

407

AN:

1268

East Asian (EAS)

AF:

0.0806

AC:

330

AN:

4094

South Asian (SAS)

AF:

0.273

AC:

3067

AN:

11226

European-Finnish (FIN)

AF:

0.522

AC:

2669

AN:

5116

Middle Eastern (MID)

AF:

0.309

AC:

AN:

256

European-Non Finnish (NFE)

AF:

0.474

AC:

17731

AN:

37402

Other (OTH)

AF:

0.405

AC:

1339

AN:

3308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.409

Heterozygous variant carriers

632

1265

1897

2530

3162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

204

306

408

510

<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:

0.437

AC:

66524

AN:

152062

Hom.:

17938

Cov.:

AF XY:

0.433

AC XY:

32191

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.153

AC:

6353

AN:

41498

American (AMR)

AF:

0.374

AC:

5705

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.503

AC:

1746

AN:

3470

East Asian (EAS)

AF:

0.130

AC:

672

AN:

5176

South Asian (SAS)

AF:

0.428

AC:

2065

AN:

4822

European-Finnish (FIN)

AF:

0.620

AC:

6539

AN:

10542

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.618

AC:

42015

AN:

67970

Other (OTH)

AF:

0.442

AC:

932

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1576

3152

4729

6305

7881

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

608

1216

1824

2432

3040

<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:

0.379

Hom.:

2968

Bravo

AF:

0.406

Asia WGS

AF:

0.249

AC:

867

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

2.9

(source)

DANN

Benign

0.58

PhyloP100

3.6

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