14-67722667-ACCT-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM4_SupportingBS1_SupportingBS2
The NM_152443.3(RDH12):c.29_31delCCT(p.Ser10del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000737 in 1,613,814 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152443.3 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RDH12 | NM_152443.3 | c.29_31delCCT | p.Ser10del | disruptive_inframe_deletion | Exon 3 of 9 | ENST00000551171.6 | NP_689656.2 | |
RDH12 | XM_047430965.1 | c.29_31delCCT | p.Ser10del | disruptive_inframe_deletion | Exon 3 of 9 | XP_047286921.1 | ||
GPHN | XM_047430879.1 | c.1313-12524_1313-12522delCCT | intron_variant | Intron 14 of 14 | XP_047286835.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.29_31delCCT | p.Ser10del | disruptive_inframe_deletion | Exon 3 of 9 | 1 | NM_152443.3 | ENSP00000449079.1 | ||
RDH12 | ENST00000267502.3 | c.29_31delCCT | p.Ser10del | disruptive_inframe_deletion | Exon 2 of 8 | 5 | ENSP00000267502.3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251142Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135742
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461642Hom.: 3 AF XY: 0.000118 AC XY: 86AN XY: 727136
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74330
ClinVar
Submissions by phenotype
Leber congenital amaurosis Uncertain:1
- -
Leber congenital amaurosis 13 Uncertain:1
This variant, c.29_31del, results in the deletion of 1 amino acid(s) of the RDH12 protein (p.Ser10del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs754556714, gnomAD 0.09%). This variant has not been reported in the literature in individuals affected with RDH12-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at