rs764710670
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM4BP6
The NM_001379500.1(COL18A1):c.1800_1808del(p.Pro603_Pro605del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000531 in 1,486,532 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00098 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00048 ( 4 hom. )
Consequence
COL18A1
NM_001379500.1 inframe_deletion
NM_001379500.1 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.83
Genes affected
COL18A1 (HGNC:2195): (collagen type XVIII alpha 1 chain) This gene encodes the alpha chain of type XVIII collagen. This collagen is one of the multiplexins, extracellular matrix proteins that contain multiple triple-helix domains (collagenous domains) interrupted by non-collagenous domains. A long isoform of the protein has an N-terminal domain that is homologous to the extracellular part of frizzled receptors. Proteolytic processing at several endogenous cleavage sites in the C-terminal domain results in production of endostatin, a potent antiangiogenic protein that is able to inhibit angiogenesis and tumor growth. Mutations in this gene are associated with Knobloch syndrome. The main features of this syndrome involve retinal abnormalities, so type XVIII collagen may play an important role in retinal structure and in neural tube closure. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_001379500.1.
BP6
?
Variant 21-45486944-CCCCCCTGGG-C is Benign according to our data. Variant chr21-45486944-CCCCCCTGGG-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 447115.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=1}. Variant chr21-45486944-CCCCCCTGGG-C is described in Lovd as [Likely_benign]. Variant chr21-45486944-CCCCCCTGGG-C is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL18A1 | NM_001379500.1 | c.1800_1808del | p.Pro603_Pro605del | inframe_deletion | 16/42 | ENST00000651438.1 | |
COL18A1 | NM_030582.4 | c.2340_2348del | p.Pro783_Pro785del | inframe_deletion | 15/41 | ||
COL18A1 | NM_130444.3 | c.3045_3053del | p.Pro1018_Pro1020del | inframe_deletion | 15/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL18A1 | ENST00000651438.1 | c.1800_1808del | p.Pro603_Pro605del | inframe_deletion | 16/42 | NM_001379500.1 | |||
COL18A1 | ENST00000355480.10 | c.2340_2348del | p.Pro783_Pro785del | inframe_deletion | 15/41 | 1 | |||
COL18A1 | ENST00000359759.8 | c.3045_3053del | p.Pro1018_Pro1020del | inframe_deletion | 15/41 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000967 AC: 147AN: 151956Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000766 AC: 82AN: 107000Hom.: 1 AF XY: 0.000735 AC XY: 43AN XY: 58514
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GnomAD4 exome AF: 0.000480 AC: 641AN: 1334458Hom.: 4 AF XY: 0.000468 AC XY: 307AN XY: 656280
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GnomAD4 genome ? AF: 0.000980 AC: 149AN: 152074Hom.: 1 Cov.: 33 AF XY: 0.00113 AC XY: 84AN XY: 74352
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 17, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 14, 2024 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at