12-1952517-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_152640.5(DCP1B):​c.1423G>A​(p.Ala475Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000378 in 1,614,000 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 Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000041 ( 0 hom. )

Consequence

DCP1B
NM_152640.5 missense

Scores

4
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.18
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.25068438).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DCP1BNM_152640.5 linkc.1423G>A p.Ala475Thr missense_variant 7/9 ENST00000280665.11 NP_689853.3 Q8IZD4-1
DCP1BNR_135060.2 linkn.1575G>A non_coding_transcript_exon_variant 8/11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DCP1BENST00000280665.11 linkc.1423G>A p.Ala475Thr missense_variant 7/91 NM_152640.5 ENSP00000280665.6 Q8IZD4-1
DCP1BENST00000540622.1 linkc.1045G>A p.Ala349Thr missense_variant 4/55 ENSP00000444374.1 F5GZK9
DCP1BENST00000543381.5 linkn.*1189G>A non_coding_transcript_exon_variant 8/105 ENSP00000445011.1 F5H4R4
DCP1BENST00000543381.5 linkn.*1189G>A 3_prime_UTR_variant 8/105 ENSP00000445011.1 F5H4R4

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152134
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000517
AC:
13
AN:
251452
Hom.:
0
AF XY:
0.0000515
AC XY:
7
AN XY:
135898
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000176
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000410
AC:
60
AN:
1461866
Hom.:
0
Cov.:
35
AF XY:
0.0000316
AC XY:
23
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.000268
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000396
Gnomad4 OTH exome
AF:
0.0000331
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152134
Hom.:
0
Cov.:
32
AF XY:
0.0000135
AC XY:
1
AN XY:
74328
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000264
ExAC
AF:
0.0000247
AC:
3

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 10, 2024The c.1423G>A (p.A475T) alteration is located in exon 7 (coding exon 7) of the DCP1B gene. This alteration results from a G to A substitution at nucleotide position 1423, causing the alanine (A) at amino acid position 475 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Benign
-0.25
T
BayesDel_noAF
Benign
-0.30
CADD
Uncertain
26
DANN
Uncertain
1.0
DEOGEN2
Benign
0.086
T;.
Eigen
Benign
0.15
Eigen_PC
Benign
0.075
FATHMM_MKL
Uncertain
0.91
D
M_CAP
Benign
0.016
T
MetaRNN
Benign
0.25
T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.1
M;.
PrimateAI
Benign
0.48
T
PROVEAN
Benign
-1.4
N;N
REVEL
Benign
0.13
Sift
Uncertain
0.0070
D;D
Sift4G
Benign
0.28
T;D
Polyphen
0.99
D;.
Vest4
0.52
MutPred
0.35
Gain of catalytic residue at L480 (P = 0.0072);.;
MVP
0.33
MPC
0.30
ClinPred
0.16
T
GERP RS
4.7
Varity_R
0.10
gMVP
0.32

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.

Other links and lift over

dbSNP: rs757747292; hg19: chr12-2061683; API