rs10505725

Positions:

• chr12-1947197-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152640.5(DCP1B):​c.1774-911G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,014 control chromosomes in the GnomAD database, including 5,707 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 0.26 (5707 hom., cov: 32)
• Consequence: DCP1B NM_152640.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.628

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCP1B	NM_152640.5	c.1774-911G>A		intron_variant		ENST00000280665.11	NP_689853.3
DCP1B	NR_135060.2	n.1926-911G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCP1B	ENST00000280665.11	c.1774-911G>A		intron_variant		1	NM_152640.5	ENSP00000280665	P1
DCP1B	ENST00000543381.5	c.*1540-911G>A		intron_variant, NMD_transcript_variant		5		ENSP00000445011

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40200 AN: 151898 Hom.: 5708 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.270

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.265 AC: 40219 AN: 152014 Hom.: 5707 Cov.: 32 AF XY: 0.265 AC XY: 19708 AN XY: 74302

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.272

Alfa AF: 0.284 Hom.: 6469

Bravo AF: 0.261

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.045
DANN	Benign	0.68
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Other links and lift over

dbSNP: rs10505725; hg19: chr12-2056363;