rs2282437
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000494.4(COL17A1):c.3208+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 1,613,628 control chromosomes in the GnomAD database, including 531,264 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.72 ( 41630 hom., cov: 32)
Exomes 𝑓: 0.82 ( 489634 hom. )
Consequence
COL17A1
NM_000494.4 intron
NM_000494.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.972
Genes affected
COL17A1 (HGNC:2194): (collagen type XVII alpha 1 chain) This gene encodes the alpha chain of type XVII collagen. Unlike most collagens, collagen XVII is a transmembrane protein. Collagen XVII is a structural component of hemidesmosomes, multiprotein complexes at the dermal-epidermal basement membrane zone that mediate adhesion of keratinocytes to the underlying membrane. Mutations in this gene are associated with both generalized atrophic benign and junctional epidermolysis bullosa. Two homotrimeric forms of type XVII collagen exist. The full length form is the transmembrane protein. A soluble form, referred to as either ectodomain or LAD-1, is generated by proteolytic processing of the full length form. [provided by RefSeq, Jul 2008]
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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=-0.87).
BP6
?
Variant 10-104037620-G-A is Benign according to our data. Variant chr10-104037620-G-A is described in ClinVar as [Benign]. Clinvar id is 256272.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-104037620-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL17A1 | NM_000494.4 | c.3208+16C>T | intron_variant | ENST00000648076.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL17A1 | ENST00000648076.2 | c.3208+16C>T | intron_variant | NM_000494.4 | A2 | ||||
COL17A1 | ENST00000369733.8 | c.3073+16C>T | intron_variant | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.724 AC: 110057AN: 151974Hom.: 41637 Cov.: 32
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GnomAD3 exomes AF: 0.784 AC: 197028AN: 251384Hom.: 78425 AF XY: 0.786 AC XY: 106844AN XY: 135876
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GnomAD4 exome AF: 0.816 AC: 1192267AN: 1461536Hom.: 489634 Cov.: 51 AF XY: 0.814 AC XY: 591564AN XY: 727074
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GnomAD4 genome ? AF: 0.724 AC: 110070AN: 152092Hom.: 41630 Cov.: 32 AF XY: 0.723 AC XY: 53781AN XY: 74344
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Junctional epidermolysis bullosa, non-Herlitz type Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Epithelial recurrent erosion dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 22, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at