9-113461775-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000350696.9(RGS3):c.149G>T(p.Cys50Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000681 in 1,614,124 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
ENST00000350696.9 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 |
---|---|---|---|---|---|---|---|
RGS3 | NM_144488.8 | c.-164G>T | 5_prime_UTR_variant | 3/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS3 | ENST00000350696.9 | c.149G>T | p.Cys50Phe | missense_variant | 2/25 | 5 | A2 | ||
RGS3 | ENST00000374140.6 | c.149G>T | p.Cys50Phe | missense_variant | 3/26 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000721 AC: 18AN: 249566Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135396
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461824Hom.: 0 Cov.: 32 AF XY: 0.0000605 AC XY: 44AN XY: 727214
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74474
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at