rs117582762
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_018127.7(ELAC2):c.1692C>T(p.Arg564Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000494 in 1,596,304 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_018127.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELAC2 | NM_018127.7 | c.1692C>T | p.Arg564Arg | synonymous_variant | Exon 18 of 24 | ENST00000338034.9 | NP_060597.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00136 AC: 302AN: 221690Hom.: 3 AF XY: 0.00102 AC XY: 121AN XY: 119200
GnomAD4 exome AF: 0.000495 AC: 715AN: 1443938Hom.: 9 Cov.: 33 AF XY: 0.000468 AC XY: 335AN XY: 716322
GnomAD4 genome AF: 0.000486 AC: 74AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.000577 AC XY: 43AN XY: 74508
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Prostate cancer, hereditary, 2 Benign:1
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ELAC2-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Combined oxidative phosphorylation defect type 17 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at