8-42861868-G-GA
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_030954.4(RNF170):c.397-14dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000409 in 1,571,552 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000086 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00044 ( 0 hom. )
Consequence
RNF170
NM_030954.4 intron
NM_030954.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.475
Genes affected
RNF170 (HGNC:25358): (ring finger protein 170) This gene encodes a RING domain-containing protein that resides in the endoplasmic reticulum (ER) membrane. This protein functions as an E3 ubiquitin ligase and mediates ubiquitination and processing of inositol 1,4,5-trisphosphate (IP3) receptors via the ER-associated protein degradation pathway. It is recruited to the activated IP3 receptors by the ERLIN1/ERLIN2 complex to which it is constitutively bound. Mutations in this gene are associated with autosomal dominant sensory ataxia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
BP6
Variant 8-42861868-G-GA is Benign according to our data. Variant chr8-42861868-G-GA is described in ClinVar as [Likely_benign]. Clinvar id is 1284587.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000861 AC: 13AN: 151000Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000444 AC: 630AN: 1420440Hom.: 0 Cov.: 28 AF XY: 0.000450 AC XY: 318AN XY: 705934
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GnomAD4 genome AF: 0.0000860 AC: 13AN: 151112Hom.: 0 Cov.: 32 AF XY: 0.000122 AC XY: 9AN XY: 73732
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
not provided Benign:2
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
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Clinical Genetics, Academic Medical Center
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
- -
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at