13-41458321-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014059.3(RGCC):c.86C>G(p.Ser29Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000757 in 1,584,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014059.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RGCC | NM_014059.3 | c.86C>G | p.Ser29Trp | missense_variant | Exon 2 of 5 | ENST00000379359.4 | NP_054778.2 | |
RGCC | XM_047430282.1 | c.86C>G | p.Ser29Trp | missense_variant | Exon 2 of 3 | XP_047286238.1 | ||
RGCC | XR_007063677.1 | n.244C>G | non_coding_transcript_exon_variant | Exon 2 of 4 | ||||
RGCC | XR_941565.2 | n.244C>G | non_coding_transcript_exon_variant | Exon 2 of 4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000247 AC: 5AN: 202210Hom.: 0 AF XY: 0.0000178 AC XY: 2AN XY: 112054
GnomAD4 exome AF: 0.00000768 AC: 11AN: 1432454Hom.: 0 Cov.: 31 AF XY: 0.00000562 AC XY: 4AN XY: 711598
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.86C>G (p.S29W) alteration is located in exon 2 (coding exon 2) of the RGCC gene. This alteration results from a C to G substitution at nucleotide position 86, causing the serine (S) at amino acid position 29 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