NM_024422.6:c.2126G>T

Variant names:

• chr18-31070850-C-A
• NM_024422.6:c.2126G>T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_024422.6(DSC2):​c.2126G>T​(p.Cys709Phe) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DSC2 NM_024422.6 missense, splice_region
• Scores: Splicing: ADA: 0.9994
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.71

Genes affected

DSC2 (HGNC:3036): (desmocollin 2) This gene encodes a member of the desmocollin protein subfamily. Desmocollins, along with desmogleins, are cadherin-like transmembrane glycoproteins that are major components of the desmosome. Desmosomes are cell-cell junctions that help resist shearing forces and are found in high concentrations in cells subject to mechanical stress. This gene is found in a cluster with other desmocollin family members on chromosome 18. Mutations in this gene are associated with arrhythmogenic right ventricular dysplasia-11, and reduced protein expression has been described in several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSC2	NM_024422.6	c.2126G>T	p.Cys709Phe	missense_variant, splice_region_variant	Exon 14 of 16	ENST00000280904.11	NP_077740.1
DSC2	NM_004949.5	c.2126G>T	p.Cys709Phe	missense_variant, splice_region_variant	Exon 14 of 17		NP_004940.1
DSC2	NM_001406506.1	c.1697G>T	p.Cys566Phe	missense_variant, splice_region_variant	Exon 14 of 16		NP_001393435.1
DSC2	NM_001406507.1	c.1697G>T	p.Cys566Phe	missense_variant, splice_region_variant	Exon 14 of 17		NP_001393436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSC2	ENST00000280904.11	c.2126G>T	p.Cys709Phe	missense_variant, splice_region_variant	Exon 14 of 16	1	NM_024422.6	ENSP00000280904.6
DSC2	ENST00000251081.8	c.2126G>T	p.Cys709Phe	missense_variant, splice_region_variant	Exon 14 of 17	1		ENSP00000251081.6
DSC2	ENST00000648081.1	c.1697G>T	p.Cys566Phe	missense_variant, splice_region_variant	Exon 15 of 17			ENSP00000497441.1
DSC2	ENST00000682357.1	c.1697G>T	p.Cys566Phe	missense_variant, splice_region_variant	Exon 14 of 16			ENSP00000507826.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.38	T;.;.
Eigen	Uncertain	0.59
Eigen_PC	Uncertain	0.58
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Uncertain	0.89	D;D;D
M_CAP	Benign	0.061	D
MetaRNN	Uncertain	0.69	D;D;D
MetaSVM	Benign	-0.29	T
MutationAssessor	Uncertain	2.6	M;M;.
PrimateAI	Benign	0.41	T
PROVEAN	Pathogenic	-6.8	D;D;.
REVEL	Benign	0.29
Sift	Uncertain	0.010	D;D;.
Sift4G	Uncertain	0.0090	D;D;.
Polyphen		0.85	P;D;.
Vest4		0.51
MutPred		0.46		Gain of helix (P = 0.027);Gain of helix (P = 0.027);.;
MVP		0.88
MPC		0.47
ClinPred		0.88	D
GERP RS		6.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.20
gMVP		0.77

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.89
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

No publications associated with this variant yet.

Other links and lift over

hg19: chr18-28650816;