chr17-13011784-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PVS1_ModerateBP6BS1BS2
The NM_018127.7(ELAC2):c.560-2A>G variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000468 in 1,614,178 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_018127.7 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ELAC2 | NM_018127.7 | c.560-2A>G | splice_acceptor_variant, intron_variant | Intron 6 of 23 | ENST00000338034.9 | NP_060597.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00258 AC: 392AN: 152172Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000696 AC: 175AN: 251456Hom.: 1 AF XY: 0.000552 AC XY: 75AN XY: 135904
GnomAD4 exome AF: 0.000249 AC: 364AN: 1461888Hom.: 2 Cov.: 33 AF XY: 0.000204 AC XY: 148AN XY: 727244
GnomAD4 genome AF: 0.00257 AC: 391AN: 152290Hom.: 3 Cov.: 32 AF XY: 0.00251 AC XY: 187AN XY: 74474
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 18, 2020 | This variant is associated with the following publications: (PMID: 26046366) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jan 11, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | ELAC2: BS2 - |
Combined oxidative phosphorylation defect type 17 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at