rs8131523
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001379500.1(COL18A1):c.106+17055C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 520,730 control chromosomes in the GnomAD database, including 5,299 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 2454 hom., cov: 33)
Exomes 𝑓: 0.12 ( 2845 hom. )
Consequence
COL18A1
NM_001379500.1 intron
NM_001379500.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.187
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 Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL18A1 | NM_001379500.1 | c.106+17055C>T | intron_variant | ENST00000651438.1 | |||
COL18A1-AS1 | NR_027498.1 | n.321G>A | non_coding_transcript_exon_variant | 2/3 | |||
COL18A1-AS1 | NR_028082.1 | n.1405G>A | non_coding_transcript_exon_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL18A1 | ENST00000651438.1 | c.106+17055C>T | intron_variant | NM_001379500.1 | |||||
COL18A1-AS1 | ENST00000397787.5 | n.1405G>A | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
COL18A1-AS1 | ENST00000485206.1 | n.321G>A | non_coding_transcript_exon_variant | 2/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.160 AC: 24263AN: 152118Hom.: 2454 Cov.: 33
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GnomAD3 exomes AF: 0.129 AC: 28582AN: 221864Hom.: 2102 AF XY: 0.125 AC XY: 15052AN XY: 120042
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GnomAD4 exome AF: 0.116 AC: 42910AN: 368494Hom.: 2845 Cov.: 0 AF XY: 0.116 AC XY: 24294AN XY: 209438
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GnomAD4 genome ? AF: 0.160 AC: 24283AN: 152236Hom.: 2454 Cov.: 33 AF XY: 0.161 AC XY: 11982AN XY: 74438
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at