chr14-67722648-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_152443.3(RDH12):c.6G>C(p.Leu2=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L2L) has been classified as Likely benign.
Frequency
Consequence
NM_152443.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDH12 | NM_152443.3 | c.6G>C | p.Leu2= | synonymous_variant | 3/9 | ENST00000551171.6 | |
RDH12 | XM_047430965.1 | c.6G>C | p.Leu2= | synonymous_variant | 3/9 | ||
GPHN | XM_047430879.1 | c.1313-12547G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.6G>C | p.Leu2= | synonymous_variant | 3/9 | 1 | NM_152443.3 | P1 | |
RDH12 | ENST00000267502.3 | c.6G>C | p.Leu2= | synonymous_variant | 2/8 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251170Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135742
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461408Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727034
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Leber congenital amaurosis 13 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at