chr9-113483116-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001394167.1(RGS3):āc.188A>Cā(p.Lys63Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000033 in 1,606,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001394167.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS3 | NM_001394167.1 | c.188A>C | p.Lys63Thr | missense_variant, splice_region_variant | 3/23 | ENST00000695401.1 | |
RGS3 | NM_144488.8 | c.212A>C | p.Lys71Thr | missense_variant, splice_region_variant | 6/26 | ||
RGS3 | NM_001282923.2 | c.194A>C | p.Lys65Thr | missense_variant, splice_region_variant | 3/23 | ||
RGS3 | NM_017790.6 | c.188A>C | p.Lys63Thr | missense_variant, splice_region_variant | 3/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS3 | ENST00000695401.1 | c.188A>C | p.Lys63Thr | missense_variant, splice_region_variant | 3/23 | NM_001394167.1 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250508Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135364
GnomAD4 exome AF: 0.0000351 AC: 51AN: 1454694Hom.: 0 Cov.: 28 AF XY: 0.0000552 AC XY: 40AN XY: 724172
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at