rs828616

chr3-98822272-G-Achr3-98822272-G-Cchr3-98822272-G-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Moderate BP7 BA1

The NM_080927.4(DCBLD2):c.786C>T(p.Ile262=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,612,904 control chromosomes in the GnomAD database, including 106,864 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 0.31 (8642 hom., cov: 33)
  • Exomes 𝑓: 0.36 (98222 hom.)
• Consequence: DCBLD2 NM_080927.4 synonymous
• 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 Benign. Variant got -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BP7: Synonymous conserved (PhyloP=2.07 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCBLD2	NM_080927.4	c.786C>T	p.Ile262=	synonymous_variant	6/16	ENST00000326840.11
DCBLD2	XM_011512419.3	c.558C>T	p.Ile186=	synonymous_variant	5/15
DCBLD2	XM_024453348.2	c.468C>T	p.Ile156=	synonymous_variant	6/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCBLD2	ENST00000326840.11	c.786C>T	p.Ile262=	synonymous_variant	6/16	1	NM_080927.4	P1
DCBLD2	ENST00000326857.9	c.786C>T	p.Ile262=	synonymous_variant	6/16	1
DCBLD2	ENST00000469648.5			downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46911 AN: 151960 Hom.: 8642 Cov.: 33

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.340

GnomAD3 exomes AF: 0.393 AC: 97567 AN: 248176 Hom.: 21188 AF XY: 0.392 AC XY: 52797 AN XY: 134630

Gnomad AFR exome AF: 0.116

Gnomad AMR exome AF: 0.532

Gnomad ASJ exome AF: 0.353

Gnomad EAS exome AF: 0.689

Gnomad SAS exome AF: 0.407

Gnomad FIN exome AF: 0.369

Gnomad NFE exome AF: 0.346

Gnomad OTH exome AF: 0.396

GnomAD4 exome AF: 0.357 AC: 521596 AN: 1460826 Hom.: 98222 Cov.: 39 AF XY: 0.359 AC XY: 260793 AN XY: 726716

Gnomad4 AFR exome AF: 0.110

Gnomad4 AMR exome AF: 0.520

Gnomad4 ASJ exome AF: 0.351

Gnomad4 EAS exome AF: 0.694

Gnomad4 SAS exome AF: 0.404

Gnomad4 FIN exome AF: 0.367

Gnomad4 NFE exome AF: 0.342

Gnomad4 OTH exome AF: 0.359

GnomAD4 genome AF: 0.309 AC: 46919 AN: 152078 Hom.: 8642 Cov.: 33 AF XY: 0.314 AC XY: 23354 AN XY: 74328

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.341

Alfa AF: 0.346 Hom.: 12342

Bravo AF: 0.309

Asia WGS AF: 0.523 AC: 1816 AN: 3478

EpiCase AF: 0.353

EpiControl AF: 0.363

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
Cadd	Benign	8.7
Dann	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs828616; hg19: chr3-98541116; COSMIC: COSV58789838; COSMIC: COSV58789838;