Variant 3-53292112-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018403.7(DCP1A):c.1340C>T(p.Ala447Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00326 in 1,613,578 control chromosomes in the GnomAD database, including 228 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0056 ( 32 hom., cov: 32)

Exomes 𝑓: 0.0030 ( 196 hom. )

Consequence

DCP1A
NM_018403.7 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.333

Variant links:

Genes affected

DCP1A (HGNC:18714): (decapping mRNA 1A) Decapping is a key step in general and regulated mRNA decay. The protein encoded by this gene is a decapping enzyme. This protein and another decapping enzyme form a decapping complex, which interacts with the nonsense-mediated decay factor hUpf1 and may be recruited to mRNAs containing premature termination codons. This protein also participates in the TGF-beta signaling pathway. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]

DCP1A links:

LOC107986087 (HGNC:):

LOC107986087 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0023297668).

BP6

Variant 3-53292112-G-A is Benign according to our data. Variant chr3-53292112-G-A is described in ClinVar as [Benign]. Clinvar id is 770142.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCP1A	NM_018403.7 linkuse as main transcript	c.1340C>T	p.Ala447Val	missense_variant	7/10	ENST00000610213.6	NP_060873.4
LOC107986087	XR_001740702.3 linkuse as main transcript	n.208-787G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCP1A	ENST00000610213.6 linkuse as main transcript	c.1340C>T	p.Ala447Val	missense_variant	7/10	1	NM_018403.7	ENSP00000476386	P1	Q9NPI6-1
DCP1A	ENST00000294241.10 linkuse as main transcript	c.1226C>T	p.Ala409Val	missense_variant	6/9	2		ENSP00000476046		Q9NPI6-2

Frequencies

GnomAD3 genomes

AF:

0.00552

AC:

839

AN:

151934

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00160

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0471

Gnomad ASJ

AF:

0.00116

Gnomad EAS

AF:

0.00560

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000946

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000147

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.0125

AC:

3100

AN:

248746

Hom.:

156

AF XY:

0.00958

AC XY:

1293

AN XY:

134930

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.0853

Gnomad ASJ exome

AF:

0.000398

Gnomad EAS exome

AF:

0.00390

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000798

Gnomad OTH exome

AF:

0.00894

GnomAD4 exome

AF:

0.00302

AC:

4413

AN:

1461526

Hom.:

196

Cov.:

AF XY:

0.00264

AC XY:

1918

AN XY:

727032

show subpopulations

Gnomad4 AFR exome

AF:

0.000986

Gnomad4 AMR exome

AF:

0.0821

Gnomad4 ASJ exome

AF:

0.000459

Gnomad4 EAS exome

AF:

0.0122

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000459

Gnomad4 OTH exome

AF:

0.00265

GnomAD4 genome

AF:

0.00559

AC:

850

AN:

152052

Hom.:

Cov.:

AF XY:

0.00603

AC XY:

448

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.00159

Gnomad4 AMR

AF:

0.0478

Gnomad4 ASJ

AF:

0.00116

Gnomad4 EAS

AF:

0.00562

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000946

Gnomad4 NFE

AF:

0.000147

Gnomad4 OTH

AF:

0.00522

Alfa

AF:

0.000800

Hom.:

Bravo

AF:

0.00956

ESP6500AA

AF:

0.000962

AC:

ESP6500EA

AF:

0.000356

AC:

ExAC

AF:

0.00905

AC:

1096

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0000545

EpiControl

AF:

0.000296

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 30, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.54

CADD

Benign

6.4

DANN

Benign

0.73

DEOGEN2

Benign

0.016

T;.

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.70

T;T

MetaRNN

Benign

0.0023

T;T

MutationAssessor

Benign

1.1

L;.

PrimateAI

Benign

0.38

Sift4G

Benign

0.58

T;T

Polyphen

0.0

B;.

Vest4

0.16

GERP RS

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.055

gMVP

0.31

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