chr5-139476373-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_198282.4(STING1):c.1028T>C(p.Val343Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,460,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V343M) has been classified as Uncertain significance.
Frequency
Consequence
NM_198282.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STING1 | NM_198282.4 | c.1028T>C | p.Val343Ala | missense_variant | 8/8 | ENST00000330794.9 | |
STING1 | NM_001301738.2 | c.841T>C | p.Trp281Arg | missense_variant | 7/7 | ||
STING1 | NM_001367258.1 | c.671T>C | p.Val224Ala | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STING1 | ENST00000330794.9 | c.1028T>C | p.Val343Ala | missense_variant | 8/8 | 1 | NM_198282.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460506Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726552
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
STING-associated vasculopathy with onset in infancy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 21, 2023 | This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 343 of the TMEM173 protein (p.Val343Ala). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TMEM173-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at