chr13-98177233-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_178861.5(RNF113B):c.4G>C(p.Ala2Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000458 in 1,549,474 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.4G>C | p.Ala2Pro | missense_variant | 1/2 | ENST00000267291.7 | |
FARP1 | NM_005766.4 | c.-24+33741C>G | intron_variant | ENST00000319562.11 | |||
FARP1 | NM_001001715.4 | c.-24+33741C>G | intron_variant | ||||
FARP1 | NM_001286839.2 | c.-24+34456C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF113B | ENST00000267291.7 | c.4G>C | p.Ala2Pro | missense_variant | 1/2 | 1 | NM_178861.5 | P1 | |
FARP1 | ENST00000319562.11 | c.-24+33741C>G | intron_variant | 1 | NM_005766.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000740 AC: 15AN: 202822Hom.: 0 AF XY: 0.000101 AC XY: 11AN XY: 109006
GnomAD4 exome AF: 0.0000494 AC: 69AN: 1397294Hom.: 2 Cov.: 34 AF XY: 0.0000799 AC XY: 55AN XY: 688766
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2023 | The c.4G>C (p.A2P) alteration is located in exon 1 (coding exon 1) of the RNF113B gene. This alteration results from a G to C substitution at nucleotide position 4, causing the alanine (A) at amino acid position 2 to be replaced by a proline (P). 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