chr12-6943851-C-T
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NR_023317.1(RNU7-1):n.36C>T 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 0.00303 in 900,868 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0056 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0025 ( 9 hom. )
Consequence
RNU7-1
NR_023317.1 non_coding_transcript_exon
NR_023317.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.256
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 Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 12-6943851-C-T is Benign according to our data. Variant chr12-6943851-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1301230.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 6 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNU7-1 | NR_023317.1 | n.36C>T | non_coding_transcript_exon_variant | 1/1 | |||
C12orf57 | NM_001301834.1 | c.-16+189C>T | intron_variant | ||||
C12orf57 | NM_001301836.2 | c.13+189C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNU7-1 | ENST00000458811.1 | n.36C>T | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000607421.2 | n.780G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00555 AC: 845AN: 152140Hom.: 6 Cov.: 33
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GnomAD4 exome AF: 0.00252 AC: 1884AN: 748610Hom.: 9 Cov.: 10 AF XY: 0.00243 AC XY: 914AN XY: 375634
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GnomAD4 genome AF: 0.00556 AC: 846AN: 152258Hom.: 6 Cov.: 33 AF XY: 0.00524 AC XY: 390AN XY: 74466
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | RNU7-1: BS1, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at