4-168878047-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000507735.6(PALLD):c.156G>A(p.Ser52Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000901 in 1,331,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S52S) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000090 ( 0 hom. )

Consequence

PALLD
ENST00000507735.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.117

Publications

0 publications found

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:

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]

CBR4 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 4-168878047-G-A is Benign according to our data. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-168878047-G-A is described in CliVar as Likely_benign. Clinvar id is 135998.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.117 with no splicing effect.

BS2

High AC in GnomAdExome4 at 12 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PALLD	NM_001166108.2 link	c.1965-12875G>A		intron_variant	Intron 10 of 21	ENST00000505667.6	NP_001159580.1	Q8WX93-9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PALLD	ENST00000505667.6 link	c.1965-12875G>A		intron_variant	Intron 10 of 21	1	NM_001166108.2	ENSP00000425556.1		Q8WX93-9

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000236

AC:

AN:

84804

AF XY:

0.0000415

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000901

AC:

AN:

1331582

Hom.:

Cov.:

AF XY:

0.0000152

AC XY:

AN XY:

656484

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26906

American (AMR)

AF:

0.00

AC:

AN:

28786

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

23434

East Asian (EAS)

AF:

0.00

AC:

AN:

29516

South Asian (SAS)

AF:

0.000148

AC:

AN:

74166

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33046

Middle Eastern (MID)

AF:

0.000199

AC:

AN:

5016

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1055314

Other (OTH)

AF:

0.00

AC:

AN:

55398

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Pancreatic adenocarcinoma

Benign:1

Aug 15, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

8.5

(source)

DANN

Benign

0.94

PhyloP100

0.12

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over