rs79026338
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001374736.1(DST):c.3492C>T(p.Asn1164=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.0021 in 1,614,070 control chromosomes in the GnomAD database, including 59 homozygotes. 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: 𝑓 0.011 ( 25 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 34 hom. )
Consequence
DST
NM_001374736.1 splice_region, synonymous
NM_001374736.1 splice_region, synonymous
Scores
2
Splicing: ADA: 0.8814
2
Clinical Significance
Conservation
PhyloP100: 5.45
Genes affected
DST (HGNC:1090): (dystonin) This gene encodes a member of the plakin protein family of adhesion junction plaque proteins. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene, but the full-length nature of some variants has not been defined. It has been reported that some isoforms are expressed in neural and muscle tissue, anchoring neural intermediate filaments to the actin cytoskeleton, and some isoforms are expressed in epithelial tissue, anchoring keratin-containing intermediate filaments to hemidesmosomes. Consistent with the expression, mice defective for this gene show skin blistering and neurodegeneration. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 6-56634464-G-A is Benign according to our data. Variant chr6-56634464-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 357606.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-56634464-G-A is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0109 (1660/152232) while in subpopulation AFR AF= 0.0379 (1572/41532). AF 95% confidence interval is 0.0363. There are 25 homozygotes in gnomad4. There are 778 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DST | NM_001374736.1 | c.3492C>T | p.Asn1164= | splice_region_variant, synonymous_variant | 26/104 | ENST00000680361.1 | |
DST | NM_001723.7 | c.1881C>T | p.Asn627= | splice_region_variant, synonymous_variant | 12/24 | ENST00000370765.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DST | ENST00000680361.1 | c.3492C>T | p.Asn1164= | splice_region_variant, synonymous_variant | 26/104 | NM_001374736.1 | |||
DST | ENST00000370765.11 | c.1881C>T | p.Asn627= | splice_region_variant, synonymous_variant | 12/24 | 1 | NM_001723.7 |
Frequencies
GnomAD3 genomes ? AF: 0.0109 AC: 1659AN: 152114Hom.: 25 Cov.: 32
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GnomAD3 exomes AF: 0.00315 AC: 793AN: 251408Hom.: 11 AF XY: 0.00222 AC XY: 301AN XY: 135872
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GnomAD4 exome AF: 0.00119 AC: 1737AN: 1461838Hom.: 34 Cov.: 32 AF XY: 0.000975 AC XY: 709AN XY: 727206
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GnomAD4 genome ? AF: 0.0109 AC: 1660AN: 152232Hom.: 25 Cov.: 32 AF XY: 0.0105 AC XY: 778AN XY: 74424
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Hereditary sensory and autonomic neuropathy type 6;C3809470:Epidermolysis bullosa simplex 3, localized or generalized intermediate, with BP230 deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Hereditary sensory and autonomic neuropathy type 6 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at