14-67729195-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_152443.3(RDH12):c.663C>T(p.Thr221=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,612,638 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. T221T) has been classified as Uncertain significance.
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.663C>T | p.Thr221= | synonymous_variant | 8/9 | ENST00000551171.6 | |
RDH12 | XM_047430965.1 | c.663C>T | p.Thr221= | synonymous_variant | 8/9 | ||
ZFYVE26 | XM_047431173.1 | c.*547G>A | 3_prime_UTR_variant | 42/42 | |||
GPHN | XM_047430879.1 | c.1313-6000C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.663C>T | p.Thr221= | synonymous_variant | 8/9 | 1 | NM_152443.3 | P1 | |
RDH12 | ENST00000267502.3 | c.663C>T | p.Thr221= | synonymous_variant | 7/8 | 5 | P1 | ||
RDH12 | ENST00000552873.1 | n.32C>T | non_coding_transcript_exon_variant | 2/2 | 5 | ||||
ZFYVE26 | ENST00000394455.6 | n.3288+16G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248932Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134848
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460502Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726628
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
Leber congenital amaurosis 13 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at