13-98177158-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178861.5(RNF113B):c.79C>T(p.Arg27Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,607,142 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R27L) has been classified as Uncertain significance.
Frequency
Consequence
NM_178861.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF113B | NM_178861.5 | c.79C>T | p.Arg27Trp | missense_variant | 1/2 | ENST00000267291.7 | |
FARP1 | NM_005766.4 | c.-24+33666G>A | intron_variant | ENST00000319562.11 | |||
FARP1 | NM_001001715.4 | c.-24+33666G>A | intron_variant | ||||
FARP1 | NM_001286839.2 | c.-24+34381G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF113B | ENST00000267291.7 | c.79C>T | p.Arg27Trp | missense_variant | 1/2 | 1 | NM_178861.5 | P1 | |
FARP1 | ENST00000319562.11 | c.-24+33666G>A | intron_variant | 1 | NM_005766.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000163 AC: 4AN: 245914Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133282
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1455024Hom.: 1 Cov.: 34 AF XY: 0.0000166 AC XY: 12AN XY: 723934
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 12, 2023 | The c.79C>T (p.R27W) alteration is located in exon 1 (coding exon 1) of the RNF113B gene. This alteration results from a C to T substitution at nucleotide position 79, causing the arginine (R) at amino acid position 27 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at