rs558493564
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_030954.4(RNF170):c.397-14delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,576,324 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00020 ( 0 hom. )
Consequence
RNF170
NM_030954.4 intron
NM_030954.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
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-GA-G is Benign according to our data. Variant chr8-42861868-GA-G is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000795 AC: 12AN: 151004Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.000203 AC: 290AN: 1425320Hom.: 0 Cov.: 28 AF XY: 0.000199 AC XY: 141AN XY: 708410
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GnomAD4 genome AF: 0.0000795 AC: 12AN: 151004Hom.: 0 Cov.: 32 AF XY: 0.0000679 AC XY: 5AN XY: 73614
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ClinVar
Not reported inComputational 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