rs16928961

Variant names:

• chr12-1949158-C-T
• rs16928961
• NM_152640.5:c.1701G>A

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_Strong BP6_Very_Strong BP7 BA1

The NM_152640.5(DCP1B):​c.1701G>A​(p.Pro567Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00487 in 1,614,056 control chromosomes in the GnomAD database, including 343 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.026 (172 hom., cov: 33)
  • Exomes 𝑓: 0.0027 (171 hom.)
• Consequence: DCP1B NM_152640.5 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.34
• Publications: 2 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 -21 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 12-1949158-C-T is Benign according to our data. Variant chr12-1949158-C-T is described in ClinVar as Benign. ClinVar VariationId is 776685.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-2.34 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0879 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCP1B	NM_152640.5	MANE Select	c.1701G>A	p.Pro567Pro	synonymous	Exon 8 of 9	NP_689853.3
	DCP1B	NR_135060.2		n.1853G>A		non_coding_transcript_exon	Exon 9 of 11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCP1B	ENST00000280665.11	TSL:1 MANE Select	c.1701G>A	p.Pro567Pro	synonymous	Exon 8 of 9	ENSP00000280665.6	Q8IZD4-1
	DCP1B	ENST00000971563.1		c.1701G>A	p.Pro567Pro	synonymous	Exon 8 of 10	ENSP00000641622.1
	DCP1B	ENST00000883051.1		c.1782G>A	p.Pro594Pro	synonymous	Exon 8 of 9	ENSP00000553110.1

Frequencies

GnomAD3 genomes AF: 0.0259 AC: 3942 AN: 152104 Hom.: 172 Cov.: 33

Gnomad AFR AF: 0.0905

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00930

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000162

Gnomad OTH AF: 0.0192

GnomAD2 exomes AF: 0.00695 AC: 1740 AN: 250284 AF XY: 0.00478

Gnomad AFR exome AF: 0.0945

Gnomad AMR exome AF: 0.00489

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000106

Gnomad OTH exome AF: 0.00376

GnomAD4 exome AF: 0.00267 AC: 3910 AN: 1461834 Hom.: 171 Cov.: 34 AF XY: 0.00225 AC XY: 1634 AN XY: 727216

African (AFR) AF: 0.0959 AC: 3209 AN: 33478

American (AMR) AF: 0.00546 AC: 244 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.0000383 AC: 1 AN: 26136

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39700

South Asian (SAS) AF: 0.000186 AC: 16 AN: 86248

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53408

Middle Eastern (MID) AF: 0.00347 AC: 20 AN: 5758

European-Non Finnish (NFE) AF: 0.0000674 AC: 75 AN: 1111996

Other (OTH) AF: 0.00570 AC: 344 AN: 60390

GnomAD4 genome AF: 0.0259 AC: 3947 AN: 152222 Hom.: 172 Cov.: 33 AF XY: 0.0253 AC XY: 1887 AN XY: 74446

African (AFR) AF: 0.0903 AC: 3750 AN: 41524

American (AMR) AF: 0.00929 AC: 142 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000829 AC: 4 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000162 AC: 11 AN: 68016

Other (OTH) AF: 0.0190 AC: 40 AN: 2110

Alfa AF: 0.00965 Hom.: 97

Bravo AF: 0.0303

Asia WGS AF: 0.00346 AC: 12 AN: 3478

EpiCase AF: 0.0000545

EpiControl AF: 0.000119

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.48
DANN	Benign	0.51
PhyloP100		-2.3
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: rs16928961; hg19: chr12-2058324;