12-6943867-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NR_023317.1(RNU7-1):n.52C>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 0.0181 in 939,128 control chromosomes in the GnomAD database, including 186 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.015 ( 20 hom., cov: 33)
Exomes 𝑓: 0.019 ( 166 hom. )
Consequence
RNU7-1
NR_023317.1 non_coding_transcript_exon
NR_023317.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.752
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 12-6943867-C-T is Benign according to our data. Variant chr12-6943867-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1301050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0154 (2344/152260) while in subpopulation AMR AF= 0.0223 (341/15294). AF 95% confidence interval is 0.0203. There are 20 homozygotes in gnomad4. There are 1077 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 20 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNU7-1 | NR_023317.1 | n.52C>T | non_coding_transcript_exon_variant | 1/1 | |||
C12orf57 | NM_001301834.1 | c.-16+205C>T | intron_variant | ||||
C12orf57 | NM_001301836.2 | c.13+205C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNU7-1 | ENST00000458811.1 | n.52C>T | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000607421.2 | n.764G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0154 AC: 2343AN: 152142Hom.: 20 Cov.: 33
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GnomAD4 exome AF: 0.0186 AC: 14674AN: 786868Hom.: 166 Cov.: 10 AF XY: 0.0187 AC XY: 7373AN XY: 394480
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GnomAD4 genome AF: 0.0154 AC: 2344AN: 152260Hom.: 20 Cov.: 33 AF XY: 0.0145 AC XY: 1077AN XY: 74440
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2021 | - - |
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