chr5-178320690-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_173465.4(COL23A1):c.362-13771A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,182 control chromosomes in the GnomAD database, including 2,434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).
Frequency
Genomes: 𝑓 0.15 ( 2434 hom., cov: 33)
Consequence
COL23A1
NM_173465.4 intron
NM_173465.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.88
Genes affected
COL23A1 (HGNC:22990): (collagen type XXIII alpha 1 chain) COL23A1 is a member of the transmembrane collagens, a subfamily of the nonfibrillar collagens that contain a single pass hydrophobic transmembrane domain (Banyard et al., 2003 [PubMed 12644459]).[supplied by OMIM, Mar 2008]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL23A1 | NM_173465.4 | c.362-13771A>G | intron_variant | ENST00000390654.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL23A1 | ENST00000390654.8 | c.362-13771A>G | intron_variant | 5 | NM_173465.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.149 AC: 22656AN: 152064Hom.: 2433 Cov.: 33
GnomAD3 genomes
?
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22656
AN:
152064
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.149 AC: 22656AN: 152182Hom.: 2434 Cov.: 33 AF XY: 0.159 AC XY: 11863AN XY: 74406
GnomAD4 genome
?
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AC:
22656
AN:
152182
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33
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11863
AN XY:
74406
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Asia WGS
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1321
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3478
ClinVar
Significance: association
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Vascular endothelial growth factor (VEGF) inhibitor response Other:1
association, no assertion criteria provided | case-control | Department of Ophthalmology, College of Medicine, Hanyang University | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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