rs10022002

Variant names:

• chr4-168563061-G-A
• rs10022002
• NM_001166108.2:c.908+50649G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-168563061-G-A
• chr4-168563061-G-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.908+50649G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,992 control chromosomes in the GnomAD database, including 28,867 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 0.61 (28867 hom., cov: 31)
• Consequence: PALLD NM_001166108.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• 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

LOC124900807 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.775 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.908+50649G>A		intron	N/A	NP_001159580.1	Q8WX93-9
	PALLD	NM_016081.4		c.908+50649G>A		intron	N/A	NP_057165.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PALLD	ENST00000505667.6	TSL:1 MANE Select	c.908+50649G>A		intron	N/A	ENSP00000425556.1	Q8WX93-9
	PALLD	ENST00000261509.10	TSL:1	c.908+50649G>A		intron	N/A	ENSP00000261509.6	Q8WX93-2
	PALLD	ENST00000968439.1		c.908+50649G>A		intron	N/A	ENSP00000638498.1

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93274 AN: 151874 Hom.: 28842 Cov.: 31

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.795

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.614 AC: 93345 AN: 151992 Hom.: 28867 Cov.: 31 AF XY: 0.617 AC XY: 45851 AN XY: 74290

African (AFR) AF: 0.560 AC: 23210 AN: 41438

American (AMR) AF: 0.609 AC: 9303 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2059 AN: 3464

East Asian (EAS) AF: 0.795 AC: 4110 AN: 5168

South Asian (SAS) AF: 0.571 AC: 2751 AN: 4822

European-Finnish (FIN) AF: 0.709 AC: 7503 AN: 10576

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.621 AC: 42193 AN: 67944

Other (OTH) AF: 0.602 AC: 1270 AN: 2110

Alfa AF: 0.617 Hom.: 11415

Bravo AF: 0.605

Asia WGS AF: 0.650 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.80
PhyloP100		0.12
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: rs10022002; hg19: chr4-169484212;