NM_001303461.1:c.-297+886T>C
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_001303461.1(OVOL2):c.-297+886T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
OVOL2
NM_001303461.1 intron
NM_001303461.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.16
Publications
3 publications found
Genes affected
OVOL2 (HGNC:15804): (ovo like zinc finger 2) This gene encodes a member of the evolutionarily conserved ovo-like protein family. Mammalian members of this family contain a single zinc finger domain composed of a tetrad of C2H2 zinc fingers with variable N- and C-terminal extensions that contain intrinsically disordered domains. Members of this family are involved in epithelial development and differentiation. Knockout of this gene in mouse results in early embryonic lethality with phenotypes that include neurectoderm expansion, impaired vascularization, and heart anomalies. In humans, allelic variants of this gene have been associated with posterior polymorphous corneal dystrophy. [provided by RefSeq, Apr 2016]
OVOL2 Gene-Disease associations (from GenCC):
- posterior polymorphous corneal dystrophy 1Inheritance: AD Classification: DEFINITIVE, STRONG, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- congenital hereditary endothelial dystrophy type IInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- posterior polymorphous corneal dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 20-18058004-A-G is Pathogenic according to our data. Variant chr20-18058004-A-G is described in ClinVar as Pathogenic. ClinVar VariationId is 224838.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34). . Strength limited to SUPPORTING due to the PP5.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001303461.1. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 278026Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 136008
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
278026
Hom.:
AF XY:
AC XY:
0
AN XY:
136008
African (AFR)
AF:
AC:
0
AN:
6410
American (AMR)
AF:
AC:
0
AN:
3006
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5442
East Asian (EAS)
AF:
AC:
0
AN:
8872
South Asian (SAS)
AF:
AC:
0
AN:
7866
European-Finnish (FIN)
AF:
AC:
0
AN:
8282
Middle Eastern (MID)
AF:
AC:
0
AN:
898
European-Non Finnish (NFE)
AF:
AC:
0
AN:
224176
Other (OTH)
AF:
AC:
0
AN:
13074
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:no assertion criteria provided
Pathogenic
VUS
Benign
Condition
1
-
-
Posterior polymorphous corneal dystrophy 1 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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