chr17-76158415-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_052916.3(RNF157):c.1391C>T(p.Pro464Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,612,554 control chromosomes in the GnomAD database, including 124 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0076 ( 8 hom., cov: 32)
Exomes 𝑓: 0.011 ( 116 hom. )
Consequence
RNF157
NM_052916.3 missense
NM_052916.3 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -0.277
Genes affected
RNF157 (HGNC:29402): (ring finger protein 157) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of signal transduction; positive regulation of dendrite extension; and protein autoubiquitination. Predicted to be located in cell body. Predicted to be active in early endosome; nucleus; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.004362017).
BP6
Variant 17-76158415-G-A is Benign according to our data. Variant chr17-76158415-G-A is described in ClinVar as [Benign]. Clinvar id is 791506.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF157 | NM_052916.3 | c.1391C>T | p.Pro464Leu | missense_variant | 13/19 | ENST00000269391.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF157 | ENST00000269391.11 | c.1391C>T | p.Pro464Leu | missense_variant | 13/19 | 1 | NM_052916.3 | P4 | |
RNF157 | ENST00000647930.1 | c.1391C>T | p.Pro464Leu | missense_variant | 13/19 | A1 | |||
RNF157 | ENST00000319945.10 | c.1391C>T | p.Pro464Leu | missense_variant | 13/18 | 2 | |||
RNF157 | ENST00000592869.1 | n.109C>T | non_coding_transcript_exon_variant | 1/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00757 AC: 1152AN: 152088Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00729 AC: 1832AN: 251160Hom.: 11 AF XY: 0.00700 AC XY: 950AN XY: 135768
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GnomAD4 exome AF: 0.0110 AC: 16124AN: 1460348Hom.: 116 Cov.: 30 AF XY: 0.0106 AC XY: 7682AN XY: 726570
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GnomAD4 genome AF: 0.00757 AC: 1152AN: 152206Hom.: 8 Cov.: 32 AF XY: 0.00690 AC XY: 513AN XY: 74394
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;N
MutationTaster
Benign
N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.;N
REVEL
Benign
Sift
Benign
T;.;T
Sift4G
Benign
T;.;T
Polyphen
B;.;B
Vest4
MVP
MPC
ClinPred
T
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Splicing
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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