rs566806

chr12-91165420-G-Achr12-91165420-G-T

Variant summary

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

The NM_001920.5(DCN):c.212-703C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,916 control chromosomes in the GnomAD database, including 12,823 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 0.37 (12823 hom., cov: 32)
• Consequence: DCN NM_001920.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.701

Genes affected

DCN (HGNC:2705): (decorin) This gene encodes a member of the small leucine-rich proteoglycan family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. This protein plays a role in collagen fibril assembly. Binding of this protein to multiple cell surface receptors mediates its role in tumor suppression, including a stimulatory effect on autophagy and inflammation and an inhibitory effect on angiogenesis and tumorigenesis. This gene and the related gene biglycan are thought to be the result of a gene duplication. Mutations in this gene are associated with congenital stromal corneal dystrophy in human patients. [provided by RefSeq, Nov 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DCN	NM_001920.5	c.212-703C>T		intron_variant		ENST00000052754.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DCN	ENST00000052754.10	c.212-703C>T		intron_variant		1	NM_001920.5	P1

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56764 AN: 151802 Hom.: 12791 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.372

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.374 AC: 56856 AN: 151916 Hom.: 12823 Cov.: 32 AF XY: 0.368 AC XY: 27311 AN XY: 74224

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.345

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.372

Alfa AF: 0.293 Hom.: 3457

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.40

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: rs566806; hg19: chr12-91559197;