4-168687639-C-T

Variant names:

• chr4-168687639-C-T
• rs17054480
• NM_001166108.2:c.1335+2080C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001166108.2(PALLD):​c.1335+2080C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,260 control chromosomes in the GnomAD database, including 268 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 0.055 (268 hom., cov: 32)
• Consequence: PALLD NM_001166108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 2 publications found

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 Gene-Disease associations (from GenCC):

• pancreatic cancer, susceptibility to, 1

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALLD	NM_001166108.2	c.1335+2080C>T		intron_variant	Intron 6 of 21	ENST00000505667.6	NP_001159580.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALLD	ENST00000505667.6	c.1335+2080C>T		intron_variant	Intron 6 of 21	1	NM_001166108.2	ENSP00000425556.1

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8430 AN: 152142 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.0329

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0716

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0521

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0555 AC: 8444 AN: 152260 Hom.: 268 Cov.: 32 AF XY: 0.0555 AC XY: 4129 AN XY: 74452

African (AFR) AF: 0.0877 AC: 3643 AN: 41554

American (AMR) AF: 0.0328 AC: 502 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3468

East Asian (EAS) AF: 0.0396 AC: 205 AN: 5182

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4824

European-Finnish (FIN) AF: 0.0716 AC: 759 AN: 10596

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0438 AC: 2979 AN: 68020

Other (OTH) AF: 0.0520 AC: 110 AN: 2114

Alfa AF: 0.0475 Hom.: 452

Bravo AF: 0.0541

Asia WGS AF: 0.0350 AC: 121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.40
PhyloP100		0.026
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17054480; hg19: chr4-169608790;