chr13-98176351-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_178861.5(RNF113B):c.886C>T(p.Pro296Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P296L) has been classified as Uncertain significance.
Frequency
Consequence
NM_178861.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF113B | NM_178861.5 | c.886C>T | p.Pro296Ser | missense_variant | 1/2 | ENST00000267291.7 | |
FARP1 | NM_005766.4 | c.-24+32859G>A | intron_variant | ENST00000319562.11 | |||
FARP1 | NM_001001715.4 | c.-24+32859G>A | intron_variant | ||||
FARP1 | NM_001286839.2 | c.-24+33574G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF113B | ENST00000267291.7 | c.886C>T | p.Pro296Ser | missense_variant | 1/2 | 1 | NM_178861.5 | P1 | |
FARP1 | ENST00000319562.11 | c.-24+32859G>A | intron_variant | 1 | NM_005766.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.