12-1951414-A-G

Position:

• chr12-1951414-A-G

Variant summary

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

The NM_152640.5(DCP1B):​c.1524+1002T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,164 control chromosomes in the GnomAD database, including 29,458 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 0.61 (29458 hom., cov: 33)
• Consequence: DCP1B NM_152640.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCP1B	NM_152640.5	c.1524+1002T>C		intron_variant		ENST00000280665.11	NP_689853.3
DCP1B	NR_135060.2	n.1676+1002T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCP1B	ENST00000280665.11	c.1524+1002T>C		intron_variant		1	NM_152640.5	ENSP00000280665.6
DCP1B	ENST00000540622.1	c.1146+1002T>C		intron_variant		5		ENSP00000444374.1
DCP1B	ENST00000543381.5	n.*1290+1002T>C		intron_variant		5		ENSP00000445011.1

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92318 AN: 152046 Hom.: 29416 Cov.: 33

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.607 AC: 92414 AN: 152164 Hom.: 29458 Cov.: 33 AF XY: 0.601 AC XY: 44715 AN XY: 74382

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.607

Alfa AF: 0.540 Hom.: 46425

Bravo AF: 0.620

Asia WGS AF: 0.597 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.50

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: rs6489338; hg19: chr12-2060580;