4-168497248-TA-T

Position:

• chr4-168497248-TA-T

Variant summary

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

The NM_001166108.2(PALLD):​c.-83+67delA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (14003 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: PALLD NM_001166108.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.807

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]

DDX60L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 4-168497248-TA-T is Benign according to our data. Variant chr4-168497248-TA-T is described in ClinVar as [Benign]. Clinvar id is 1245061.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PALLD	NM_001166108.2	c.-83+67delA		intron_variant		ENST00000505667.6	NP_001159580.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PALLD	ENST00000505667.6	c.-83+67delA		intron_variant		1	NM_001166108.2	ENSP00000425556.1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 64491 AN: 147060 Hom.: 13991 Cov.: 0

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.439 AC: 64542 AN: 147124 Hom.: 14003 Cov.: 0 AF XY: 0.443 AC XY: 31719 AN XY: 71542

Gnomad4 AFR AF: 0.452

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.440

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 30, 2019

- -

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: rs34221810; hg19: chr4-169418399;