ENST00000507699.1:n.3748delA

Variant names:

• chr4-168928326-TA-T
• rs398064261
• ENST00000507699.1:n.3748delA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000507699.1(PALLD):​n.3748delA variant causes a non coding transcript exon 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 ENST00000507699.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.04
• Publications: 1 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]

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

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
PALLD	NM_001166108.2	c.*2156delA		3_prime_UTR_variant	Exon 22 of 22	ENST00000505667.6	NP_001159580.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALLD	ENST00000505667.6	c.*2156delA		3_prime_UTR_variant	Exon 22 of 22	1	NM_001166108.2	ENSP00000425556.1

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

African (AFR) AF: 0.465 AC: 443 AN: 952

American (AMR) AF: 0.726 AC: 446 AN: 614

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 1248 AN: 1776

East Asian (EAS) AF: 0.942 AC: 5192 AN: 5512

South Asian (SAS) AF: 0.781 AC: 175 AN: 224

European-Finnish (FIN) AF: 0.794 AC: 351 AN: 442

Middle Eastern (MID) AF: 0.709 AC: 122 AN: 172

European-Non Finnish (NFE) AF: 0.733 AC: 11730 AN: 16012

Other (OTH) AF: 0.691 AC: 1583 AN: 2292

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

African (AFR) AF: 0.438 AC: 17990 AN: 41048

American (AMR) AF: 0.704 AC: 10712 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2407 AN: 3470

East Asian (EAS) AF: 0.954 AC: 4917 AN: 5152

South Asian (SAS) AF: 0.788 AC: 3790 AN: 4810

European-Finnish (FIN) AF: 0.803 AC: 8407 AN: 10472

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50688 AN: 67912

Other (OTH) AF: 0.686 AC: 1444 AN: 2104

Alfa AF: 0.660 Hom.: 1399

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Carcinoma of pancreas Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.0
Mutation Taster		=99/1	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: rs398064261; hg19: chr4-169849477; COSMIC: COSV54971964; COSMIC: COSV54971964;