12-6943845-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_001301834.1(C12orf57):c.-16+183A>G variant causes a intron change. The variant allele was found at a frequency of 0.0000682 in 893,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_001301834.1 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C12orf57 | NM_001301834.1 | c.-16+183A>G | intron_variant | Intron 1 of 3 | NP_001288763.1 | |||
C12orf57 | NM_001301836.2 | c.13+183A>G | intron_variant | Intron 1 of 2 | NP_001288765.1 | |||
RNU7-1 | NR_023317.1 | n.30A>G | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C12orf57 | ENST00000544681 | c.-277A>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 2 | 2 | ENSP00000475422.1 | ||||
C12orf57 | ENST00000537087 | c.-277A>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 3 | 2 | ENSP00000440937.1 | ||||
C12orf57 | ENST00000544681 | c.-277A>G | 5_prime_UTR_variant | Exon 1 of 2 | 2 | ENSP00000475422.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152230Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000742 AC: 55AN: 741664Hom.: 0 Cov.: 10 AF XY: 0.0000833 AC XY: 31AN XY: 372056
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74374
ClinVar
Submissions by phenotype
Aicardi-Goutieres syndrome 9 Pathogenic:1
The RNU7-1 g.7053008A>G variant (chr12, hg19), also referred to as RNU7-1 (NR_023317.1) n.30A>G, is a non-coding transcript exon variant that has been reported in a four year old boy of European Russian descent with Aicardi-Goutieres syndrome in a compound heterozygous state with a second RNU7-1 variant, n.34_41del (Uggenti et al. 2020). The n.30A>G variant is reported at a frequency of 0.000065 in the European Non-Finnish population of the Genome Aggregation Database (version 2.1.1), an allele frequency consistent with a rare autosomal recessive disorder. The n.30A>G variant is located within the noncanonical Sm-binding site of U7 snRNA, a region which determines the assembly of the U7snRNP (Stefanovic et al. 1995). Using a chimeric mouse histone H4 pre-mRNA-U7 snRNA construct, in a xenopus oocyte in vitro system, Kolev et al. showed that substitution of alternative nucleotides at n.30A abolished pre-mRNA processing (Kolev et al. 2006). Based the evidence, the n.30A>G variant is classified as likely pathogenic for Aicardi-Goutieres syndrome. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at