chr12-6943852-T-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NR_023317.1(RNU7-1):n.37T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000994 in 905,712 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
RNU7-1
NR_023317.1 non_coding_transcript_exon
NR_023317.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.536
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNU7-1 | NR_023317.1 | n.37T>G | non_coding_transcript_exon_variant | 1/1 | |||
C12orf57 | NM_001301834.1 | c.-16+190T>G | intron_variant | ||||
C12orf57 | NM_001301836.2 | c.13+190T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNU7-1 | ENST00000458811.1 | n.37T>G | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000607421.2 | n.779A>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000104 AC: 78AN: 753532Hom.: 0 Cov.: 10 AF XY: 0.0000952 AC XY: 36AN XY: 378124
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GnomAD4 genome AF: 0.0000789 AC: 12AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74350
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Sep 01, 2022 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at