rs558493564

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.475
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RNF170NM_030954.4 linkc.397-14delT intron_variant Intron 5 of 6 ENST00000527424.6 NP_112216.3 Q96K19-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RNF170ENST00000527424.6 linkc.397-14delT intron_variant Intron 5 of 6 1 NM_030954.4 ENSP00000434797.1 Q96K19-1

Frequencies

GnomAD3 genomes
AF:
0.0000795
AC:
12
AN:
151004
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000973
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.000203
AC:
290
AN:
1425320
Hom.:
0
Cov.:
28
AF XY:
0.000199
AC XY:
141
AN XY:
708410
show subpopulations
Gnomad4 AFR exome
AF:
0.000157
Gnomad4 AMR exome
AF:
0.000153
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000516
Gnomad4 SAS exome
AF:
0.0000374
Gnomad4 FIN exome
AF:
0.0000779
Gnomad4 NFE exome
AF:
0.000241
Gnomad4 OTH exome
AF:
0.000102
GnomAD4 genome
AF:
0.0000795
AC:
12
AN:
151004
Hom.:
0
Cov.:
32
AF XY:
0.0000679
AC XY:
5
AN XY:
73614
show subpopulations
Gnomad4 AFR
AF:
0.0000973
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000434
Hom.:
1
Bravo
AF:
0.0000491

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs558493564; hg19: chr8-42717011; API