NM_004415.4:c.598-4G>T

Variant names:

• chr6-7562648-G-T
• NM_004415.4:c.598-4G>T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_004415.4(DSP):​c.598-4G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: DSP NM_004415.4 splice_region, intron
• Scores: Splicing: ADA: 0.00001724
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.210

Genes affected

DSP (HGNC:3052): (desmoplakin) This gene encodes a protein that anchors intermediate filaments to desmosomal plaques and forms an obligate component of functional desmosomes. Mutations in this gene are the cause of several cardiomyopathies and keratodermas, including skin fragility-woolly hair syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 6-7562648-G-T is Benign according to our data. Variant chr6-7562648-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1628936.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSP	NM_004415.4	c.598-4G>T		splice_region_variant, intron_variant	Intron 4 of 23	ENST00000379802.8	NP_004406.2
DSP	NM_001319034.2	c.598-4G>T		splice_region_variant, intron_variant	Intron 4 of 23		NP_001305963.1
DSP	NM_001008844.3	c.598-4G>T		splice_region_variant, intron_variant	Intron 4 of 23		NP_001008844.1
DSP	NM_001406591.1	c.598-4G>T		splice_region_variant, intron_variant	Intron 4 of 10		NP_001393520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSP	ENST00000379802.8	c.598-4G>T		splice_region_variant, intron_variant	Intron 4 of 23	1	NM_004415.4	ENSP00000369129.3
DSP	ENST00000418664.2	c.598-4G>T		splice_region_variant, intron_variant	Intron 4 of 23	1		ENSP00000396591.2
DSP	ENST00000710359.1	c.598-4G>T		splice_region_variant, intron_variant	Intron 4 of 23			ENSP00000518230.1
DSP	ENST00000506617.1	n.116-4G>T		splice_region_variant, intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Arrhythmogenic right ventricular dysplasia 8;C1854063:Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Benign:1

Jan 25, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000017
dbscSNV1_RF	Benign	0.0020
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: chr6-7562881;