rs2032057982

Variant names:

• chr16-67990916-C-G
• rs2032057982
• NM_022355.4:c.814G>C

Your query was ambiguous. Multiple possible variants found:

• chr16-67990916-C-G
• chr16-67990916-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_022355.4(DPEP2):​c.814G>C​(p.Glu272Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E272K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DPEP2 NM_022355.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

DPEP2 (HGNC:23028): (dipeptidase 2) DPEP2 belongs to the membrane-bound dipeptidase (EC 3.4.13.19) family. These enzymes hydrolyze a variety of dipeptides, including leukotriene D4, the beta-lactam ring of some antibiotics, and cystinyl-bis-glycine (cys-bis-gly) formed during glutathione degradation (Habib et al., 2003 [PubMed 12738806]).[supplied by OMIM, Mar 2008]

DUS2 (HGNC:26014): (dihydrouridine synthase 2) This gene encodes a cytoplasmic protein that catalyzes the conversion of uridine residues to dihydrouridine in the D-loop of tRNA. The resulting modified bases confer enhanced regional flexibility to tRNA. The encoded protein may increase the rate of translation by inhibiting an interferon-induced protein kinase. This gene has been implicated in pulmonary carcinogenesis. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.116943926).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPEP2	NM_022355.4	c.814G>C	p.Glu272Gln	missense_variant	Exon 7 of 11	ENST00000393847.6	NP_071750.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPEP2	ENST00000393847.6	c.814G>C	p.Glu272Gln	missense_variant	Exon 7 of 11	1	NM_022355.4	ENSP00000377430.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	16
DANN	Benign	0.93
DEOGEN2	Benign	0.032	T;T;T;.
Eigen	Benign	-0.73
Eigen_PC	Benign	-0.73
FATHMM_MKL	Benign	0.057	N
LIST_S2	Uncertain	0.87	.;D;D;D
M_CAP	Benign	0.00085	T
MetaRNN	Benign	0.12	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.0	L;L;.;.
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-0.33	N;.;.;.
REVEL	Benign	0.039
Sift	Benign	0.28	T;.;.;.
Sift4G	Benign	0.44	T;T;.;.
Polyphen		0.011	B;B;.;.
Vest4		0.083
MutPred		0.38		Gain of MoRF binding (P = 0.059);Gain of MoRF binding (P = 0.059);.;.;
MVP		0.14
ClinPred		0.042	T
GERP RS		0.84
Varity_R		0.14
gMVP		0.36

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: rs2032057982; hg19: chr16-68024819; COSMIC: COSV52056509; COSMIC: COSV52056509;