chr1-173828321-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_018122.5(DARS2):c.228-12C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0181 in 1,370,752 control chromosomes in the GnomAD database, including 3,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_018122.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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DARS2 | NM_018122.5 | c.228-12C>G | intron_variant | Intron 2 of 16 | ENST00000649689.2 | NP_060592.2 | ||
DARS2 | NM_001365212.1 | c.228-12C>G | intron_variant | Intron 2 of 15 | NP_001352141.1 | |||
DARS2 | NM_001365213.2 | c.228-12C>G | intron_variant | Intron 2 of 13 | NP_001352142.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0786 AC: 11595AN: 147460Hom.: 1474 Cov.: 30
GnomAD3 exomes AF: 0.0219 AC: 5479AN: 250472Hom.: 656 AF XY: 0.0165 AC XY: 2240AN XY: 135512
GnomAD4 exome AF: 0.0108 AC: 13234AN: 1223162Hom.: 1524 Cov.: 30 AF XY: 0.00958 AC XY: 5888AN XY: 614336
GnomAD4 genome AF: 0.0788 AC: 11632AN: 147590Hom.: 1478 Cov.: 30 AF XY: 0.0768 AC XY: 5522AN XY: 71922
ClinVar
Submissions by phenotype
not provided Benign:6
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This variant is associated with the following publications: (PMID: 28097321, 23065766, 27884173, 21427441) -
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Leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome Benign:4
Review of the variants reported in Reuter et al., 2017, PMID: 28097321: BS1,BS2 -
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This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at