NM_001166108.2:c.1964+6252G>A

Variant names:

• chr4-168718175-G-A
• rs7670597
• NM_001166108.2:c.1964+6252G>A

Variant summary

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

The NM_001166108.2(PALLD):​c.1964+6252G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,002 control chromosomes in the GnomAD database, including 10,774 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 0.37 (10774 hom., cov: 32)
• Consequence: PALLD NM_001166108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.462
• 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 (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166108.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PALLD	NM_001166108.2	MANE Select	c.1964+6252G>A		intron	N/A	NP_001159580.1	Q8WX93-9
	PALLD	NM_016081.4		c.1964+6252G>A		intron	N/A	NP_057165.3
	PALLD	NM_001166109.2		c.818+6252G>A		intron	N/A	NP_001159581.1	Q8WX93-8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PALLD	ENST00000505667.6	TSL:1 MANE Select	c.1964+6252G>A		intron	N/A	ENSP00000425556.1	Q8WX93-9
	PALLD	ENST00000261509.10	TSL:1	c.1964+6252G>A		intron	N/A	ENSP00000261509.6	Q8WX93-2
	PALLD	ENST00000968439.1		c.1964+6252G>A		intron	N/A	ENSP00000638498.1

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55859 AN: 151884 Hom.: 10771 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.368 AC: 55872 AN: 152002 Hom.: 10774 Cov.: 32 AF XY: 0.366 AC XY: 27182 AN XY: 74292

African (AFR) AF: 0.253 AC: 10475 AN: 41466

American (AMR) AF: 0.392 AC: 5983 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1252 AN: 3466

East Asian (EAS) AF: 0.291 AC: 1502 AN: 5164

South Asian (SAS) AF: 0.378 AC: 1824 AN: 4820

European-Finnish (FIN) AF: 0.408 AC: 4302 AN: 10548

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29161 AN: 67964

Other (OTH) AF: 0.359 AC: 758 AN: 2114

Alfa AF: 0.406 Hom.: 44127

Bravo AF: 0.362

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.46
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: rs7670597; hg19: chr4-169639326;