rs144268137
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_017831.4(RNF125):āc.387A>Gā(p.Leu129=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,613,042 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0026 ( 3 hom., cov: 32)
Exomes š: 0.0022 ( 11 hom. )
Consequence
RNF125
NM_017831.4 synonymous
NM_017831.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.58
Genes affected
RNF125 (HGNC:21150): (ring finger protein 125) This gene encodes a novel E3 ubiquitin ligase that contains a RING finger domain in the N-terminus and three zinc-binding and one ubiquitin-interacting motif in the C-terminus. As a result of myristoylation, this protein associates with membranes and is primarily localized to intracellular membrane systems. The encoded protein may function as a positive regulator in the T-cell receptor signaling pathway. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BP6
?
Variant 18-32042247-A-G is Benign according to our data. Variant chr18-32042247-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 475384.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.58 with no splicing effect.
BS2
?
High AC in GnomAd4 at 389 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF125 | NM_017831.4 | c.387A>G | p.Leu129= | synonymous_variant | 3/6 | ENST00000217740.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF125 | ENST00000217740.4 | c.387A>G | p.Leu129= | synonymous_variant | 3/6 | 1 | NM_017831.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00256 AC: 389AN: 152210Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00254 AC: 637AN: 250954Hom.: 3 AF XY: 0.00246 AC XY: 334AN XY: 135626
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GnomAD4 exome AF: 0.00224 AC: 3277AN: 1460714Hom.: 11 Cov.: 29 AF XY: 0.00213 AC XY: 1546AN XY: 726704
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GnomAD4 genome ? AF: 0.00255 AC: 389AN: 152328Hom.: 3 Cov.: 32 AF XY: 0.00321 AC XY: 239AN XY: 74494
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Tenorio syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | RNF125: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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