chr19-55048699-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001145971.2(RDH13):c.405C>T(p.Thr135=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,613,970 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 (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
RDH13
NM_001145971.2 synonymous
NM_001145971.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.13
Genes affected
RDH13 (HGNC:19978): (retinol dehydrogenase 13) This gene encodes a mitochondrial short-chain dehydrogenase/reductase, which catalyzes the reduction and oxidation of retinoids. The encoded enzyme may function in retinoic acid production and may also protect the mitochondria against oxidative stress. Alternatively spliced transcript variants have been described. [provided by RefSeq, Mar 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 19-55048699-G-A is Benign according to our data. Variant chr19-55048699-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 750430.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.13 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDH13 | NM_001145971.2 | c.405C>T | p.Thr135= | synonymous_variant | 4/7 | ENST00000415061.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDH13 | ENST00000415061.8 | c.405C>T | p.Thr135= | synonymous_variant | 4/7 | 1 | NM_001145971.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000132 AC: 20AN: 151990Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000140 AC: 35AN: 249446Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135364
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GnomAD4 exome AF: 0.000135 AC: 197AN: 1461862Hom.: 0 Cov.: 33 AF XY: 0.000140 AC XY: 102AN XY: 727242
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GnomAD4 genome AF: 0.000131 AC: 20AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74358
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 08, 2018 | - - |
Computational scores
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Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at