chr22-20241768-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_023004.6(RTN4R):c.1365C>T(p.Cys455=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000605 in 1,554,458 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 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000064 ( 0 hom. )
Consequence
RTN4R
NM_023004.6 synonymous
NM_023004.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.68
Genes affected
RTN4R (HGNC:18601): (reticulon 4 receptor) This gene encodes the receptor for reticulon 4, oligodendrocyte myelin glycoprotein and myelin-associated glycoprotein. This receptor mediates axonal growth inhibition and may play a role in regulating axonal regeneration and plasticity in the adult central nervous system. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP6
?
Variant 22-20241768-G-A is Benign according to our data. Variant chr22-20241768-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3056535.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.68 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTN4R | NM_023004.6 | c.1365C>T | p.Cys455= | synonymous_variant | 2/2 | ENST00000043402.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTN4R | ENST00000043402.8 | c.1365C>T | p.Cys455= | synonymous_variant | 2/2 | 1 | NM_023004.6 | P1 | |
RTN4R | ENST00000425986.1 | c.1623C>T | p.Cys541= | synonymous_variant | 2/2 | 2 | |||
RTN4R | ENST00000416372.5 | c.1425C>T | p.Cys475= | synonymous_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152188Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000258 AC: 4AN: 154982Hom.: 0 AF XY: 0.0000241 AC XY: 2AN XY: 82994
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GnomAD4 exome AF: 0.0000642 AC: 90AN: 1402270Hom.: 0 Cov.: 31 AF XY: 0.0000751 AC XY: 52AN XY: 692132
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
RTN4R-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at