chr5-113019971-C-G

Position:

• chr5-113019971-C-G

Variant summary

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

The ENST00000389063.3(DCP2):​c.*6487C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,080 control chromosomes in the GnomAD database, including 14,490 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 0.40 (14490 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: DCP2 ENST00000389063.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

Genes affected

DCP2 (HGNC:24452): (decapping mRNA 2) The protein encoded by this gene is a key component of an mRNA-decapping complex required for degradation of mRNAs, both in normal mRNA turnover, and in nonsense-mediated mRNA decay (NMD). It removes the 7-methyl guanine cap structure from mRNA, prior to its degradation from the 5' end. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DCP2	NM_152624.6	c.*6487C>G		3_prime_UTR_variant	11/11	ENST00000389063.3	NP_689837.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DCP2	ENST00000389063.3	c.*6487C>G		3_prime_UTR_variant	11/11	1	NM_152624.6	ENSP00000373715	P1
DCP2	ENST00000515408.5	c.*6487C>G		3_prime_UTR_variant	10/10	1		ENSP00000425770

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60532 AN: 151960 Hom.: 14487 Cov.: 33

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.446

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.398 AC: 60537 AN: 152080 Hom.: 14490 Cov.: 33 AF XY: 0.403 AC XY: 29960 AN XY: 74328

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.625

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.443

Alfa AF: 0.418 Hom.: 1905

Bravo AF: 0.395

Asia WGS AF: 0.510 AC: 1765 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	4.2
DANN	Benign	0.73

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: rs4778; hg19: chr5-112355668;