rs566806

Variant names:

• chr12-91165420-G-A
• rs566806
• NM_001920.5:c.212-703C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-91165420-G-A
• chr12-91165420-G-C
• chr12-91165420-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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]

DCN Gene-Disease associations (from GenCC):

• congenital stromal corneal dystrophy

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001920.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCN	NM_001920.5	MANE Select	c.212-703C>T		intron	N/A	NP_001911.1
	DCN	NM_133503.4		c.212-703C>T		intron	N/A	NP_598010.1
	DCN	NM_133504.3		c.212-8232C>T		intron	N/A	NP_598011.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DCN	ENST00000052754.10	TSL:1 MANE Select	c.212-703C>T		intron	N/A	ENSP00000052754.5
	DCN	ENST00000420120.6	TSL:1	c.212-8232C>T		intron	N/A	ENSP00000413723.2
	DCN	ENST00000425043.5	TSL:1	c.212-12231C>T		intron	N/A	ENSP00000401021.1

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

African (AFR) AF: 0.632 AC: 26218 AN: 41454

American (AMR) AF: 0.345 AC: 5271 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1098 AN: 3464

East Asian (EAS) AF: 0.386 AC: 1994 AN: 5170

South Asian (SAS) AF: 0.205 AC: 986 AN: 4808

European-Finnish (FIN) AF: 0.176 AC: 1860 AN: 10556

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18344 AN: 67888

Other (OTH) AF: 0.372 AC: 784 AN: 2106

Alfa AF: 0.296 Hom.: 3943

Bravo AF: 0.403

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		0.70
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: rs566806; hg19: chr12-91559197;