chr3-25501182-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP2PP3PP5_Moderate
The NM_000965.5(RARB):c.307G>T(p.Gly103Cys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/20 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_000965.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RARB | NM_000965.5 | c.307G>T | p.Gly103Cys | missense_variant, splice_region_variant | 3/8 | ENST00000330688.9 | NP_000956.2 | |
LOC124909356 | XR_007095847.1 | n.1005C>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RARB | ENST00000330688.9 | c.307G>T | p.Gly103Cys | missense_variant, splice_region_variant | 3/8 | 1 | NM_000965.5 | ENSP00000332296 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 7.07e-7 AC: 1AN: 1414994Hom.: 0 Cov.: 30 AF XY: 0.00000142 AC XY: 1AN XY: 702900
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Microphthalmia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetics Department, University Hospital of Toulouse | Oct 15, 2022 | LP (PS2, PM2, PP3) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.