rs2230687
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001379500.1(COL18A1):c.837C>A(p.Pro279=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00092 in 1,613,728 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P279P) has been classified as Benign.
Frequency
Consequence
NM_001379500.1 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL18A1 | NM_001379500.1 | c.837C>A | p.Pro279= | synonymous_variant | 6/42 | ENST00000651438.1 | |
COL18A1 | NM_130444.3 | c.2082C>A | p.Pro694= | synonymous_variant | 5/41 | ||
COL18A1 | NM_030582.4 | c.1377C>A | p.Pro459= | synonymous_variant | 5/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL18A1 | ENST00000651438.1 | c.837C>A | p.Pro279= | synonymous_variant | 6/42 | NM_001379500.1 | |||
COL18A1 | ENST00000355480.10 | c.1377C>A | p.Pro459= | synonymous_variant | 5/41 | 1 | |||
COL18A1 | ENST00000359759.8 | c.2082C>A | p.Pro694= | synonymous_variant | 5/41 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00487 AC: 740AN: 151990Hom.: 2 Cov.: 34
GnomAD3 exomes AF: 0.00117 AC: 290AN: 247204Hom.: 1 AF XY: 0.000817 AC XY: 110AN XY: 134568
GnomAD4 exome AF: 0.000508 AC: 743AN: 1461618Hom.: 3 Cov.: 33 AF XY: 0.000425 AC XY: 309AN XY: 727094
GnomAD4 genome ? AF: 0.00487 AC: 741AN: 152110Hom.: 2 Cov.: 34 AF XY: 0.00489 AC XY: 364AN XY: 74384
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 18, 2019 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
COL18A1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 22, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Knobloch syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at