chr12-6943881-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The ENST00000607421.2(ENSG00000272173):n.750A>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 0.000715 in 1,011,758 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 2 hom., cov: 34)
Exomes 𝑓: 0.00030 ( 1 hom. )
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.12
Genes affected
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
Variant 12-6943881-T-C is Benign according to our data. Variant chr12-6943881-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1314938.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C12orf57 | NM_001301834.1 | c.-16+219T>C | intron_variant | ||||
C12orf57 | NM_001301836.2 | c.13+219T>C | intron_variant | ||||
RNU7-1 | NR_023317.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000607421.2 | n.750A>G | non_coding_transcript_exon_variant | 1/1 | ||||||
RNU7-1 | ENST00000458811.1 | downstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.00304 AC: 463AN: 152242Hom.: 2 Cov.: 34
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GnomAD4 exome AF: 0.000298 AC: 256AN: 859398Hom.: 1 Cov.: 11 AF XY: 0.000263 AC XY: 113AN XY: 429702
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GnomAD4 genome AF: 0.00307 AC: 467AN: 152360Hom.: 2 Cov.: 34 AF XY: 0.00283 AC XY: 211AN XY: 74516
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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 | Apr 28, 2021 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
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