3-98822272-G-C

Variant summary

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

The NM_080927.4(DCBLD2):c.786C>G(p.Ile262Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: DCBLD2 NM_080927.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

Genes affected

DCBLD2 (HGNC:24627): (discoidin, CUB and LCCL domain containing 2) Involved in negative regulation of cell growth and wound healing. Located in cell surface. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD2	NM_080927.4	c.786C>G	p.Ile262Met	missense_variant	6/16	ENST00000326840.11
DCBLD2	XM_011512419.3	c.558C>G	p.Ile186Met	missense_variant	5/15
DCBLD2	XM_024453348.2	c.468C>G	p.Ile156Met	missense_variant	6/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD2	ENST00000326840.11	c.786C>G	p.Ile262Met	missense_variant	6/16	1	NM_080927.4	P1
DCBLD2	ENST00000326857.9	c.786C>G	p.Ile262Met	missense_variant	6/16	1
DCBLD2	ENST00000469648.5			downstream_gene_variant		3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 39

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
Cadd	Pathogenic	28
Dann	Uncertain	1.0
DEOGEN2	Uncertain	0.45	T;.
Eigen	Uncertain	0.28
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.87	D;D
M_CAP	Benign	0.060	D
MetaRNN	Uncertain	0.73	D;D
MetaSVM	Uncertain	0.33	D
MutationAssessor	Uncertain	2.3	M;M
MutationTaster	Benign	0.0013	P;P
PrimateAI	Uncertain	0.64	T
PROVEAN	Benign	-1.6	N;N
REVEL	Uncertain	0.57
Sift	Uncertain	0.010	D;D
Sift4G	Uncertain	0.017	D;D
Polyphen		0.97	D;D
Vest4		0.51
MutPred		0.38		Gain of disorder (P = 0.0828);Gain of disorder (P = 0.0828);
MVP		0.92
MPC		0.31
ClinPred		0.95	D
GERP RS		2.8
Varity_R		0.22
gMVP		0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.72		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.72		Position offset: 5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs828616; hg19: chr3-98541116;