rs7439293

chr4-168756335-G-Achr4-168756335-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.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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.62

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]

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
PALLD	NM_001166108.2	c.1964+44412G>A		intron_variant		ENST00000505667.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PALLD	ENST00000505667.6	c.1964+44412G>A		intron_variant		1	NM_001166108.2	A2
RPL9P16	ENST00000491923.1	n.520G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66538 AN: 151944 Hom.: 17944 Cov.: 32

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.: 0 AF XY: 0.371 AC XY: 15426 AN XY: 41614

Gnomad4 AFR exome AF: 0.0832

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.321

Gnomad4 EAS exome AF: 0.0806

Gnomad4 SAS exome AF: 0.273

Gnomad4 FIN exome AF: 0.522

Gnomad4 NFE exome AF: 0.474

Gnomad4 OTH exome AF: 0.405

GnomAD4 genome AF: 0.437 AC: 66524 AN: 152062 Hom.: 17938 Cov.: 32 AF XY: 0.433 AC XY: 32191 AN XY: 74342

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.620

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.442

Alfa AF: 0.477 Hom.: 2956

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
Dann	Benign	0.58

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: rs7439293; hg19: chr4-169677486; COSMIC: COSV54998418;