5-113019971-C-G

Variant names:

• chr5-113019971-C-G
• rs4778
• NM_152624.6:c.*6487C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152624.6(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 NM_152624.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 20 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DCP2	NM_152624.6	c.*6487C>G		3_prime_UTR_variant	Exon 11 of 11	ENST00000389063.3	NP_689837.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DCP2	ENST00000389063.3	c.*6487C>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_152624.6	ENSP00000373715.2
DCP2	ENST00000515408.5	c.*6487C>G		3_prime_UTR_variant	Exon 10 of 10	1		ENSP00000425770.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.119 AC: 4947 AN: 41504

American (AMR) AF: 0.548 AC: 8375 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1861 AN: 3468

East Asian (EAS) AF: 0.625 AC: 3235 AN: 5176

South Asian (SAS) AF: 0.573 AC: 2765 AN: 4826

European-Finnish (FIN) AF: 0.457 AC: 4827 AN: 10552

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33083 AN: 67964

Other (OTH) AF: 0.443 AC: 935 AN: 2112

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
PhyloP100		-0.26
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: rs4778; hg19: chr5-112355668;