chr21-45405251-G-C
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001379500.1(COL18A1):c.11+10G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000084 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000086 ( 0 hom. )
Consequence
COL18A1
NM_001379500.1 intron
NM_001379500.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.258
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 Likely_benign. Variant got -6 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 21-45405251-G-C is Benign according to our data. Variant chr21-45405251-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 2171202.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL18A1 | NM_001379500.1 | c.11+10G>C | intron_variant | ENST00000651438.1 | |||
BNAT1 | NR_183526.1 | n.197-755C>G | intron_variant, non_coding_transcript_variant | ||||
BNAT1 | NR_183527.1 | n.181+109C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL18A1 | ENST00000651438.1 | c.11+10G>C | intron_variant | NM_001379500.1 |
Frequencies
GnomAD3 genomes AF: 0.0000836 AC: 3AN: 35878Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000858 AC: 8AN: 93278Hom.: 0 Cov.: 0 AF XY: 0.000124 AC XY: 6AN XY: 48286
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GnomAD4 genome AF: 0.0000836 AC: 3AN: 35878Hom.: 0 Cov.: 0 AF XY: 0.000115 AC XY: 2AN XY: 17354
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 18, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at