4-168928326-TAAAA-TAAA

Position:

• chr4-168928326-TAAAA-TAAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001166108.2(PALLD):​c.*2156del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.67 (35550 hom., cov: 0)
  • Exomes 𝑓: 0.76 (8176 hom.)
• Consequence: PALLD NM_001166108.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.04

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]

CBR4 (HGNC:25891): (carbonyl reductase 4) Enables several functions, including 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity; NADPH binding activity; and NADPH dehydrogenase (quinone) activity. Involved in fatty acid biosynthetic process; glycoside metabolic process; and protein tetramerization. Located in mitochondrial matrix. Part of oxidoreductase complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-168928326-TA-T is Benign according to our data. Variant chr4-168928326-TA-T is described in ClinVar as [Benign]. Clinvar id is 348072.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PALLD	NM_001166108.2	c.*2156del		3_prime_UTR_variant	22/22	ENST00000505667.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PALLD	ENST00000505667.6	c.*2156del		3_prime_UTR_variant	22/22	1	NM_001166108.2	A2

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101266 AN: 151282 Hom.: 35539 Cov.: 0

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.683

GnomAD4 exome AF: 0.760 AC: 21290 AN: 27996 Hom.: 8176 Cov.: 0 AF XY: 0.766 AC XY: 9837 AN XY: 12844

Gnomad4 AFR exome AF: 0.465

Gnomad4 AMR exome AF: 0.726

Gnomad4 ASJ exome AF: 0.703

Gnomad4 EAS exome AF: 0.942

Gnomad4 SAS exome AF: 0.781

Gnomad4 FIN exome AF: 0.794

Gnomad4 NFE exome AF: 0.733

Gnomad4 OTH exome AF: 0.691

GnomAD4 genome AF: 0.669 AC: 101316 AN: 151396 Hom.: 35550 Cov.: 0 AF XY: 0.676 AC XY: 50011 AN XY: 73982

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.686

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Carcinoma of pancreas Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs398064261; hg19: chr4-169849477;