6-106572122-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_032730.5(RTN4IP1):c.1084-19A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000121 in 1,570,580 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: 32)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
RTN4IP1
NM_032730.5 intron
NM_032730.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.00100
Genes affected
RTN4IP1 (HGNC:18647): (reticulon 4 interacting protein 1) This gene encodes a mitochondrial protein that interacts with reticulon 4, which is a potent inhibitor of regeneration following spinal cord injury. This interaction may be important for reticulon-induced inhibition of neurite growth. Mutations in this gene can cause optic atrophy 10, with or without ataxia, cognitive disability, and seizures. There is a pseudogene for this gene on chromosome 12. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
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Variant 6-106572122-T-G is Benign according to our data. Variant chr6-106572122-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 1666963.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTN4IP1 | NM_032730.5 | c.1084-19A>C | intron_variant | ENST00000369063.8 | |||
RTN4IP1 | NM_001318746.1 | c.784-19A>C | intron_variant | ||||
RTN4IP1 | XM_011536192.3 | c.844-19A>C | intron_variant | ||||
RTN4IP1 | XM_017011376.3 | c.*33-19A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTN4IP1 | ENST00000369063.8 | c.1084-19A>C | intron_variant | 1 | NM_032730.5 | P1 | |||
RTN4IP1 | ENST00000539449.2 | c.*33-19A>C | intron_variant | 2 | |||||
RTN4IP1 | ENST00000493619.1 | n.82-19A>C | intron_variant, non_coding_transcript_variant | 3 | |||||
RTN4IP1 | ENST00000498091.1 | n.305-19A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152212Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243884Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132138
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GnomAD4 exome AF: 0.0000106 AC: 15AN: 1418250Hom.: 0 Cov.: 24 AF XY: 0.00000989 AC XY: 7AN XY: 707970
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74486
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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 | Jan 12, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
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Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at