rs12452285
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003835.4(RGS9):c.773C>T(p.Ser258Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00515 in 1,613,216 control chromosomes in the GnomAD database, including 138 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003835.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS9 | NM_003835.4 | c.773C>T | p.Ser258Leu | missense_variant | 12/19 | ENST00000262406.10 | |
RGS9 | NM_001081955.3 | c.764C>T | p.Ser255Leu | missense_variant | 12/19 | ||
RGS9 | NM_001165933.2 | c.764C>T | p.Ser255Leu | missense_variant | 12/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS9 | ENST00000262406.10 | c.773C>T | p.Ser258Leu | missense_variant | 12/19 | 1 | NM_003835.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00497 AC: 757AN: 152174Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00928 AC: 2316AN: 249562Hom.: 37 AF XY: 0.0105 AC XY: 1426AN XY: 135390
GnomAD4 exome AF: 0.00516 AC: 7543AN: 1460924Hom.: 124 Cov.: 30 AF XY: 0.00601 AC XY: 4366AN XY: 726842
GnomAD4 genome ? AF: 0.00505 AC: 769AN: 152292Hom.: 14 Cov.: 32 AF XY: 0.00599 AC XY: 446AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 12, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at