chr14-67727376-G-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_152443.3(RDH12):c.658+186G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0908 in 615,380 control chromosomes in the GnomAD database, including 2,740 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.090 ( 629 hom., cov: 32)
Exomes 𝑓: 0.091 ( 2111 hom. )
Consequence
RDH12
NM_152443.3 intron
NM_152443.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.252
Genes affected
RDH12 (HGNC:19977): (retinol dehydrogenase 12) The protein encoded by this gene is an NADPH-dependent retinal reductase whose highest activity is toward 9-cis and all-trans-retinol. The encoded enzyme also plays a role in the metabolism of short-chain aldehydes but does not exhibit steroid dehydrogenase activity. Defects in this gene are a cause of Leber congenital amaurosis type 13 and Retinitis Pigmentosa 53. [provided by RefSeq, Sep 2015]
ZFYVE26 (HGNC:20761): (zinc finger FYVE-type containing 26) This gene encodes a protein which contains a FYVE zinc finger binding domain. The presence of this domain is thought to target these proteins to membrane lipids through interaction with phospholipids in the membrane. Mutations in this gene are associated with autosomal recessive spastic paraplegia-15. [provided by RefSeq, Oct 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 14-67727376-G-C is Benign according to our data. Variant chr14-67727376-G-C is described in ClinVar as [Benign]. Clinvar id is 1257532.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDH12 | NM_152443.3 | c.658+186G>C | intron_variant | ENST00000551171.6 | |||
GPHN | XM_047430879.1 | c.1313-7819G>C | intron_variant | ||||
RDH12 | XM_047430965.1 | c.658+186G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDH12 | ENST00000551171.6 | c.658+186G>C | intron_variant | 1 | NM_152443.3 | P1 | |||
RDH12 | ENST00000267502.3 | c.658+186G>C | intron_variant | 5 | P1 | ||||
ZFYVE26 | ENST00000394455.6 | n.4132C>G | non_coding_transcript_exon_variant | 15/15 | 2 | ||||
RDH12 | ENST00000552873.1 | n.27+186G>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0896 AC: 13619AN: 151976Hom.: 627 Cov.: 32
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GnomAD4 exome AF: 0.0912 AC: 42265AN: 463288Hom.: 2111 Cov.: 4 AF XY: 0.0933 AC XY: 23012AN XY: 246752
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GnomAD4 genome AF: 0.0896 AC: 13623AN: 152092Hom.: 629 Cov.: 32 AF XY: 0.0913 AC XY: 6786AN XY: 74362
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 14, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at