Variant chr10-110894480-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_014456.5(PDCD4):c.1167C>T(p.Ser389=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00344 in 1,566,110 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0035 ( 16 hom. )

Consequence

PDCD4
NM_014456.5 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.826

Variant links:

Genes affected

PDCD4 (HGNC:8763): (programmed cell death 4) This gene is a tumor suppressor and encodes a protein that binds to the eukaryotic translation initiation factor 4A1 and inhibits its function by preventing RNA binding. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]

PDCD4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

BP6

Variant 10-110894480-C-T is Benign according to our data. Variant chr10-110894480-C-T is described in ClinVar as [Benign]. Clinvar id is 710229.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.826 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 16 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PDCD4	NM_014456.5 linkuse as main transcript	c.1167C>T	p.Ser389=	synonymous_variant	10/12	ENST00000280154.12
PDCD4	NM_145341.4 linkuse as main transcript	c.1134C>T	p.Ser378=	synonymous_variant	11/13
PDCD4	NM_001199492.2 linkuse as main transcript	c.1125C>T	p.Ser375=	synonymous_variant	10/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDCD4	ENST00000280154.12 linkuse as main transcript	c.1167C>T	p.Ser389=	synonymous_variant	10/12	1	NM_014456.5	P1	Q53EL6-1

Frequencies

GnomAD3 genomes

AF:

0.00306

AC:

464

AN:

151772

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000774

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.00217

Gnomad ASJ

AF:

0.0179

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00459

Gnomad OTH

AF:

0.00288

GnomAD3 exomes

AF:

0.00337

AC:

840

AN:

249148

Hom.:

AF XY:

0.00354

AC XY:

478

AN XY:

134934

show subpopulations

Gnomad AFR exome

AF:

0.000623

Gnomad AMR exome

AF:

0.00163

Gnomad ASJ exome

AF:

0.0183

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000492

Gnomad FIN exome

AF:

0.00125

Gnomad NFE exome

AF:

0.00470

Gnomad OTH exome

AF:

0.00280

GnomAD4 exome

AF:

0.00349

AC:

4930

AN:

1414220

Hom.:

Cov.:

AF XY:

0.00348

AC XY:

2455

AN XY:

706232

show subpopulations

Gnomad4 AFR exome

AF:

0.000553

Gnomad4 AMR exome

AF:

0.00171

Gnomad4 ASJ exome

AF:

0.0175

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000869

Gnomad4 FIN exome

AF:

0.00152

Gnomad4 NFE exome

AF:

0.00373

Gnomad4 OTH exome

AF:

0.00384

GnomAD4 genome

AF:

0.00305

AC:

464

AN:

151890

Hom.:

Cov.:

AF XY:

0.00279

AC XY:

207

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.000772

Gnomad4 AMR

AF:

0.00216

Gnomad4 ASJ

AF:

0.0179

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.00460

Gnomad4 OTH

AF:

0.00285

Alfa

AF:

0.00480

Hom.:

Bravo

AF:

0.00312

Asia WGS

AF:

0.000580

AC:

AN:

3464

EpiCase

AF:

0.00689

EpiControl

AF:

0.00599

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

Labcorp Genetics (formerly Invitae), Labcorp

May 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

3.9

DANN

Benign

0.51

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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