dbSNP rs12423058: DCP1B:p.Asn195Asp (chr12-1955500-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_152640.5(DCP1B):c.583A>G(p.Asn195Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,613,832 control chromosomes in the GnomAD database, including 1,112 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.026 ( 77 hom., cov: 32)

Exomes 𝑓: 0.035 ( 1035 hom. )

Consequence

DCP1B
NM_152640.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.05

Publications

12 publications found

Variant links:

Genes affected

DCP1B (HGNC:24451): (decapping mRNA 1B) This gene encodes a member of a family of proteins that function in removing the 5' cap from mRNAs, which is a step in regulated mRNA decay. This protein localizes to cytoplasmic foci which are the site of mRNA breakdown and turnover. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

DCP1B links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007843405).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0261 (3972/152296) while in subpopulation NFE AF = 0.0392 (2666/68028). AF 95% confidence interval is 0.0379. There are 77 homozygotes in GnomAd4. There are 1945 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 77 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DCP1B	NM_152640.5 link	c.583A>G	p.Asn195Asp	missense_variant	Exon 6 of 9	ENST00000280665.11	NP_689853.3	Q8IZD4-1
DCP1B	NR_135060.2 link	n.735A>G		non_coding_transcript_exon_variant	Exon 7 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCP1B	ENST00000280665.11 link	c.583A>G	p.Asn195Asp	missense_variant	Exon 6 of 9	1	NM_152640.5	ENSP00000280665.6		Q8IZD4-1

Frequencies

GnomAD3 genomes

AF:

0.0261

AC:

3974

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00613

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.0190

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00725

Gnomad FIN

AF:

0.0550

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0392

Gnomad OTH

AF:

0.0229

GnomAD2 exomes

AF:

0.0256

AC:

6442

AN:

251388

AF XY:

0.0255

show subpopulations

Gnomad AFR exome

AF:

0.00492

Gnomad AMR exome

AF:

0.0134

Gnomad ASJ exome

AF:

0.0114

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0512

Gnomad NFE exome

AF:

0.0378

Gnomad OTH exome

AF:

0.0251

GnomAD4 exome

AF:

0.0348

AC:

50789

AN:

1461536

Hom.:

1035

Cov.:

AF XY:

0.0342

AC XY:

24893

AN XY:

727080

show subpopulations

African (AFR)

AF:

0.00427

AC:

143

AN:

33474

American (AMR)

AF:

0.0145

AC:

647

AN:

44706

Ashkenazi Jewish (ASJ)

AF:

0.0111

AC:

290

AN:

26122

East Asian (EAS)

AF:

0.00

AC:

AN:

39692

South Asian (SAS)

AF:

0.00812

AC:

700

AN:

86238

European-Finnish (FIN)

AF:

0.0506

AC:

2704

AN:

53392

Middle Eastern (MID)

AF:

0.0147

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.0399

AC:

44347

AN:

1111758

Other (OTH)

AF:

0.0310

AC:

1873

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

2470

4939

7409

9878

12348

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0261

AC:

3972

AN:

152296

Hom.:

Cov.:

AF XY:

0.0261

AC XY:

1945

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.00611

AC:

254

AN:

41570

American (AMR)

AF:

0.0190

AC:

290

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0121

AC:

AN:

3468

East Asian (EAS)

AF:

0.000193

AC:

AN:

5186

South Asian (SAS)

AF:

0.00746

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0550

AC:

583

AN:

10600

Middle Eastern (MID)

AF:

0.0102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0392

AC:

2666

AN:

68028

Other (OTH)

AF:

0.0227

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

196

392

588

784

980

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0338

Hom.:

184

Bravo

AF:

0.0232

TwinsUK

AF:

0.0383

AC:

142

ALSPAC

AF:

0.0363

AC:

140

ESP6500AA

AF:

0.00862

AC:

ESP6500EA

AF:

0.0362

AC:

311

ExAC

AF:

0.0255

AC:

3098

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0352

EpiControl

AF:

0.0363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.49

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.090

T;.

Eigen

Uncertain

0.60

Eigen_PC

Uncertain

0.61

FATHMM_MKL

Uncertain

0.94

MetaRNN

Benign

0.0078

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.7

M;.

PhyloP100

3.0

PrimateAI

Benign

0.37

PROVEAN

Uncertain

-2.8

D;D

REVEL

Benign

0.083

Sift

Uncertain

0.017

D;D

Sift4G

Benign

0.12

T;T

Polyphen

0.99

D;.

Vest4

0.42

MPC

0.34

ClinPred

0.020

GERP RS

5.7

Varity_R

0.43

gMVP

0.34

Mutation Taster

=94/6

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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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rs12423058

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over