6-7555830-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004415.4(DSP):c.273+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0329 in 1,612,588 control chromosomes in the GnomAD database, including 1,038 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004415.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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DSP | NM_004415.4 | c.273+10C>T | intron_variant | Intron 2 of 23 | ENST00000379802.8 | NP_004406.2 | ||
DSP | NM_001319034.2 | c.273+10C>T | intron_variant | Intron 2 of 23 | NP_001305963.1 | |||
DSP | NM_001008844.3 | c.273+10C>T | intron_variant | Intron 2 of 23 | NP_001008844.1 | |||
DSP | NM_001406591.1 | c.273+10C>T | intron_variant | Intron 2 of 10 | NP_001393520.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0241 AC: 3665AN: 152232Hom.: 61 Cov.: 33
GnomAD3 exomes AF: 0.0235 AC: 5851AN: 249090Hom.: 101 AF XY: 0.0237 AC XY: 3188AN XY: 134764
GnomAD4 exome AF: 0.0338 AC: 49415AN: 1460238Hom.: 977 Cov.: 31 AF XY: 0.0333 AC XY: 24190AN XY: 726392
GnomAD4 genome AF: 0.0240 AC: 3664AN: 152350Hom.: 61 Cov.: 33 AF XY: 0.0221 AC XY: 1647AN XY: 74496
ClinVar
Submissions by phenotype
not specified Benign:8
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273+10C>T in intron 2 of DSP: This variant is not expected to have clinical sign ificance because it is not located in the conserved region of the splicing conse nsus sequence. 273+10C>T in intron 2 of DSP (allele frequency = 1.4%, 30/2000) -
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not provided Benign:2
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Arrhythmogenic right ventricular dysplasia 8;C1854063:Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Benign:1
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Cardiomyopathy Benign:1
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Lethal acantholytic epidermolysis bullosa Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Woolly hair-skin fragility syndrome Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Arrhythmogenic right ventricular dysplasia 8 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at