rs78233829
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_198282.4(STING1):c.689G>C(p.Gly230Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 1,613,770 control chromosomes in the GnomAD database, including 25,333 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G230S) has been classified as Uncertain significance.
Frequency
Consequence
NM_198282.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STING1 | NM_198282.4 | c.689G>C | p.Gly230Ala | missense_variant | 6/8 | ENST00000330794.9 | |
STING1 | NM_001301738.2 | c.689G>C | p.Gly230Ala | missense_variant | 6/7 | ||
STING1 | NM_001367258.1 | c.332G>C | p.Gly111Ala | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STING1 | ENST00000330794.9 | c.689G>C | p.Gly230Ala | missense_variant | 6/8 | 1 | NM_198282.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.197 AC: 29935AN: 151880Hom.: 3391 Cov.: 31
GnomAD3 exomes AF: 0.212 AC: 53220AN: 251466Hom.: 6975 AF XY: 0.203 AC XY: 27604AN XY: 135904
GnomAD4 exome AF: 0.158 AC: 231388AN: 1461772Hom.: 21927 Cov.: 36 AF XY: 0.159 AC XY: 115566AN XY: 727194
GnomAD4 genome AF: 0.197 AC: 29985AN: 151998Hom.: 3406 Cov.: 31 AF XY: 0.202 AC XY: 15034AN XY: 74274
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 48% of patients studied by a panel of primary immunodeficiencies. Number of patients: 46. Only high quality variants are reported. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | This variant is associated with the following publications: (PMID: 27927967, 24204993, 29632140) - |
STING-associated vasculopathy with onset in infancy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at