12-6943850-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NR_023317.1(RNU7-1):n.35G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0000502 in 896,030 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000051 ( 1 hom. )
Consequence
RNU7-1
NR_023317.1 non_coding_transcript_exon
NR_023317.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.70
Genes affected
RNU7-1 (HGNC:34033): (RNA, U7 small nuclear 1) Implicated in Aicardi-Goutieres syndrome. [provided by Alliance of Genome Resources, Apr 2022]
C12orf57 (HGNC:29521): (chromosome 12 open reading frame 57) This gene is ubiquitously expressed in human tissues. It is required for development of the human corpus callosum. Mutations in this gene are associated with Temtamy syndrome (TEMTYS). Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-6943850-G-A is Pathogenic according to our data. Variant chr12-6943850-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1202615.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49). . Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNU7-1 | NR_023317.1 | n.35G>A | non_coding_transcript_exon_variant | 1/1 | |||
C12orf57 | NM_001301834.1 | c.-16+188G>A | intron_variant | ||||
C12orf57 | NM_001301836.2 | c.13+188G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNU7-1 | ENST00000458811.1 | n.35G>A | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000607421.2 | n.781C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152096Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000511 AC: 38AN: 743816Hom.: 1 Cov.: 10 AF XY: 0.0000428 AC XY: 16AN XY: 373414
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74440
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Aicardi-Goutieres syndrome 9 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 16, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
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Benign
DANN
Benign
RBP_binding_hub_radar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at