rs71574716
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_139175.2(RNF133):c.3G>T(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000141 in 1,417,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
RNF133
NM_139175.2 start_lost
NM_139175.2 start_lost
Scores
3
3
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.79
Genes affected
RNF133 (HGNC:21154): (ring finger protein 133) The protein encoded by this gene contains a RING finger domain, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. This gene has no intron. [provided by RefSeq, Jul 2008]
CADPS2 (HGNC:16018): (calcium dependent secretion activator 2) This gene encodes a member of the calcium-dependent activator of secretion (CAPS) protein family, which are calcium binding proteins that regulate the exocytosis of synaptic and dense-core vesicles in neurons and neuroendocrine cells. Mutations in this gene may contribute to autism susceptibility. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PVS1
Start lost variant, no pathogenic variants between lost start and next in-frame start position. Next in-frame start position is after 19 codons. Genomic position: 122698864. Lost 0.049 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| RNF133 | ENST00000340112.3 | c.3G>T | p.Met1? | start_lost | Exon 1 of 1 | 6 | NM_139175.2 | ENSP00000344489.2 | ||
| CADPS2 | ENST00000449022.7 | c.454-35347G>T | intron_variant | Intron 2 of 29 | 5 | NM_017954.11 | ENSP00000398481.2 | |||
| CADPS2 | ENST00000412584.6 | c.454-35347G>T | intron_variant | Intron 2 of 27 | 1 | ENSP00000400401.2 | ||||
| CADPS2 | ENST00000313070.11 | c.136-35347G>T | intron_variant | Intron 2 of 29 | 5 | ENSP00000325581.8 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1417504Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 701460
GnomAD4 exome
AF:
AC:
2
AN:
1417504
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Cov.:
30
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AC XY:
0
AN XY:
701460
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ExAC
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1
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
B
Vest4
MutPred
Loss of disorder (P = 0.0682);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at