Variant chr4-168511315-CTT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001166108.2(PALLD):c.-82-107_-82-106del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 587,168 control chromosomes in the GnomAD database, including 27,086 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.29 ( 6652 hom., cov: 0)

Exomes 𝑓: 0.30 ( 20434 hom. )

Consequence

PALLD
NM_001166108.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.334

Variant links:

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]

PALLD links:

LOC107986198 (HGNC:):

LOC107986198 links:

DDX60L (HGNC:26429): (DExD/H-box 60 like) This gene encodes a member of the DExD/H-box helicase family of proteins, a subset of the super family 2 helicases. Members of the DExD/H-box helicase family share a conserved functional core comprised of two RecA-like globular domains. These domains contain conserved motifs that mediate ATP binding, ATP hydrolysis, nucleic acid binding, and RNA unwinding. In addition to functions in RNA metabolism, members of this family are involved in anti-viral immunity and act as cytosolic sensors of viral nucleic acids. The protein encoded by this gene has been shown to inhibit hepatitis C virus replication in response to interferon stimulation in cell culture. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

DDX60L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 4-168511315-CTT-C is Benign according to our data. Variant chr4-168511315-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1289336.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PALLD	NM_001166108.2 linkuse as main transcript	c.-82-107_-82-106del		intron_variant		ENST00000505667.6
LOC107986198	XR_001741448.3 linkuse as main transcript	n.281-18432_281-18431del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PALLD	ENST00000505667.6 linkuse as main transcript	c.-82-107_-82-106del		intron_variant		1	NM_001166108.2	A2	Q8WX93-9

Frequencies

GnomAD3 genomes

AF:

0.294

AC:

44664

AN:

151862

Hom.:

6645

Cov.:

show subpopulations

Gnomad AFR

AF:

0.249

Gnomad AMI

AF:

0.433

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.191

Gnomad SAS

AF:

0.223

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.330

Gnomad OTH

AF:

0.280

GnomAD4 exome

AF:

0.301

AC:

131070

AN:

435188

Hom.:

20434

AF XY:

0.297

AC XY:

68263

AN XY:

230090

show subpopulations

Gnomad4 AFR exome

AF:

0.249

Gnomad4 AMR exome

AF:

0.211

Gnomad4 ASJ exome

AF:

0.296

Gnomad4 EAS exome

AF:

0.196

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.392

Gnomad4 NFE exome

AF:

0.326

Gnomad4 OTH exome

AF:

0.295

GnomAD4 genome

AF:

0.294

AC:

44693

AN:

151980

Hom.:

6652

Cov.:

AF XY:

0.293

AC XY:

21765

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.250

Gnomad4 AMR

AF:

0.241

Gnomad4 ASJ

AF:

0.281

Gnomad4 EAS

AF:

0.190

Gnomad4 SAS

AF:

0.223

Gnomad4 FIN

AF:

0.395

Gnomad4 NFE

AF:

0.330

Gnomad4 OTH

AF:

0.276

Alfa

AF:

0.317

Hom.:

968

Bravo

AF:

0.280

Asia WGS

AF:

0.199

AC:

692

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over