chr16-269503-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_183337.3(RGS11):c.1289G>A(p.Arg430His) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000805 in 1,612,920 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R430C) has been classified as Uncertain significance.
Frequency
Consequence
NM_183337.3 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RGS11 | NM_183337.3 | c.1289G>A | p.Arg430His | missense_variant, splice_region_variant | 16/17 | ENST00000397770.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RGS11 | ENST00000397770.8 | c.1289G>A | p.Arg430His | missense_variant, splice_region_variant | 16/17 | 1 | NM_183337.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00248 AC: 378AN: 152242Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00161 AC: 401AN: 249822Hom.: 1 AF XY: 0.00167 AC XY: 226AN XY: 135482
GnomAD4 exome AF: 0.000630 AC: 920AN: 1460560Hom.: 4 Cov.: 31 AF XY: 0.000747 AC XY: 543AN XY: 726612
GnomAD4 genome ? AF: 0.00248 AC: 378AN: 152360Hom.: 2 Cov.: 33 AF XY: 0.00239 AC XY: 178AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | RGS11: PP3, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at