rs2240610

Positions:

• chr12-1948426-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.1773+660T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,096 control chromosomes in the GnomAD database, including 17,831 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 0.48 (17831 hom., cov: 33)
• Consequence: DCP1B NM_152640.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.428

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCP1B	NM_152640.5	c.1773+660T>C		intron_variant		ENST00000280665.11
DCP1B	NR_135060.2	n.1925+660T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCP1B	ENST00000280665.11	c.1773+660T>C		intron_variant		1	NM_152640.5	P1
DCP1B	ENST00000543381.5	c.*1539+660T>C		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73151 AN: 151978 Hom.: 17817 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.481 AC: 73205 AN: 152096 Hom.: 17831 Cov.: 33 AF XY: 0.478 AC XY: 35541 AN XY: 74356

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.492

Alfa AF: 0.486 Hom.: 36515

Bravo AF: 0.480

Asia WGS AF: 0.533 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.83

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: rs2240610; hg19: chr12-2057592;