chr17-12992612-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018127.7(ELAC2):c.*206C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 606,774 control chromosomes in the GnomAD database, including 105,870 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.58 ( 25330 hom., cov: 30)
Exomes 𝑓: 0.59 ( 80540 hom. )
Consequence
ELAC2
NM_018127.7 3_prime_UTR
NM_018127.7 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.22
Genes affected
ELAC2 (HGNC:14198): (elaC ribonuclease Z 2) The protein encoded by this gene has a C-terminal domain with tRNA 3′ processing endoribonuclease activity, which catalyzes the removal of the 3' trailer from precursor tRNAs. The protein also interacts with activated Smad family member 2 (Smad2) and its nuclear partner forkhead box H1 (also known as FAST-1), and reduced expression can suppress transforming growth factor-beta induced growth arrest. Mutations in this gene result in an increased risk of prostate cancer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 17-12992612-G-A is Benign according to our data. Variant chr17-12992612-G-A is described in ClinVar as [Benign]. Clinvar id is 1234592.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ELAC2 | NM_018127.7 | c.*206C>T | 3_prime_UTR_variant | 24/24 | ENST00000338034.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ELAC2 | ENST00000338034.9 | c.*206C>T | 3_prime_UTR_variant | 24/24 | 1 | NM_018127.7 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.577 AC: 87335AN: 151408Hom.: 25306 Cov.: 30
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GnomAD4 exome AF: 0.592 AC: 269642AN: 455248Hom.: 80540 Cov.: 5 AF XY: 0.590 AC XY: 140186AN XY: 237418
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GnomAD4 genome ? AF: 0.577 AC: 87408AN: 151526Hom.: 25330 Cov.: 30 AF XY: 0.577 AC XY: 42686AN XY: 74004
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at