rs2037229349
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001319074.4(RAX2):c.*897C>T variant causes a 3 prime UTR 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 Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
RAX2
NM_001319074.4 3_prime_UTR
NM_001319074.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.77
Publications
0 publications found
Genes affected
RAX2 (HGNC:18286): (retina and anterior neural fold homeobox 2) This gene encodes a homeodomain-containing protein that plays a role in eye development. Mutation of this gene causes age-related macular degeneration type 6, an eye disorder resulting in accumulations of protein and lipid beneath the retinal pigment epithelium and within the Bruch's membrane. Defects in this gene can also cause cone-rod dystrophy type 11, a disease characterized by the initial degeneration of cone photoreceptor cells and resulting in loss of color vision and visual acuity, followed by the degeneration of rod photoreceptor cells, which progresses to night blindness and the loss of peripheral vision. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
RAX2 Gene-Disease associations (from GenCC):
- retinitis pigmentosaInheritance: AR Classification: DEFINITIVE, MODERATE Submitted by: G2P, Franklin by Genoox
- cone-rod dystrophy 11Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- retinitis pigmentosa 95Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- cone-rod dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001319074.4. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 2322Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 1744
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
2322
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
1744
African (AFR)
AF:
AC:
0
AN:
34
American (AMR)
AF:
AC:
0
AN:
20
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
12
East Asian (EAS)
AF:
AC:
0
AN:
78
South Asian (SAS)
AF:
AC:
0
AN:
130
European-Finnish (FIN)
AF:
AC:
0
AN:
52
Middle Eastern (MID)
AF:
AC:
0
AN:
12
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1880
Other (OTH)
AF:
AC:
0
AN:
104
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Age related macular degeneration 6 (1)
-
1
-
Cone-rod dystrophy 11 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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