rs10022002

chr4-168563061-G-Achr4-168563061-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

LOC124900807 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PALLD	NM_001166108.2	c.908+50649G>A		intron_variant		ENST00000505667.6
LOC124900807	XR_007058359.1	n.75-25275C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PALLD	ENST00000505667.6	c.908+50649G>A		intron_variant		1	NM_001166108.2	A2
PALLD	ENST00000261509.10	c.908+50649G>A		intron_variant		1		P3
PALLD	ENST00000508898.5	c.845+50649G>A		intron_variant		2

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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.795

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.602

Alfa AF: 0.621 Hom.: 9280

Bravo AF: 0.605

Asia WGS AF: 0.650 AC: 2260 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.1
Dann	Benign	0.80

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

LitVar

Other links and lift over

dbSNP: rs10022002; hg19: chr4-169484212;