12-1951414-A-G

Variant names:

• chr12-1951414-A-G
• rs6489338
• NM_152640.5:c.1524+1002T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152640.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCP1B	NM_152640.5	MANE Select	c.1524+1002T>C		intron	N/A	NP_689853.3
	DCP1B	NR_135060.2		n.1676+1002T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCP1B	ENST00000280665.11	TSL:1 MANE Select	c.1524+1002T>C		intron	N/A	ENSP00000280665.6
	DCP1B	ENST00000540622.1	TSL:5	c.1146+1002T>C		intron	N/A	ENSP00000444374.1
	DCP1B	ENST00000543381.5	TSL:5	n.*1290+1002T>C		intron	N/A	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

African (AFR) AF: 0.815 AC: 33828 AN: 41532

American (AMR) AF: 0.503 AC: 7682 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2015 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3788 AN: 5180

South Asian (SAS) AF: 0.405 AC: 1954 AN: 4830

European-Finnish (FIN) AF: 0.496 AC: 5245 AN: 10566

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36103 AN: 67988

Other (OTH) AF: 0.607 AC: 1283 AN: 2112

Alfa AF: 0.555 Hom.: 77161

Bravo AF: 0.620

Asia WGS AF: 0.597 AC: 2079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.50
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6489338; hg19: chr12-2060580;