1-173828312-T-TGGGGGGGGGGGGGGGG

Variant names:

• chr1-173828312-T-TGGGGGGGGGGGGGGGG
• rs367543010
• NM_018122.5:c.228-21_228-20insGGGGGGGGGGGGGGGG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_018122.5(DARS2):​c.228-21_228-20insGGGGGGGGGGGGGGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000143 in 1,401,944 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 27)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: DARS2 NM_018122.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51
• Publications: 0 publications found

Genes affected

DARS2 (HGNC:25538): (aspartyl-tRNA synthetase 2, mitochondrial) The protein encoded by this gene belongs to the class-II aminoacyl-tRNA synthetase family. It is a mitochondrial enzyme that specifically aminoacylates aspartyl-tRNA. Mutations in this gene are associated with leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL). [provided by RefSeq, Nov 2009]

DARS2 Gene-Disease associations (from GenCC):

• leukoencephalopathy with brain stem and spinal cord involvement-high lactate syndrome

  Inheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Orphanet
• mitochondrial disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018122.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DARS2	NM_018122.5	MANE Select	c.228-21_228-20insGGGGGGGGGGGGGGGG		intron	N/A	NP_060592.2
	DARS2	NM_001365212.1		c.228-21_228-20insGGGGGGGGGGGGGGGG		intron	N/A	NP_001352141.1
	DARS2	NM_001365213.2		c.228-21_228-20insGGGGGGGGGGGGGGGG		intron	N/A	NP_001352142.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DARS2	ENST00000649689.2	MANE Select	c.228-21_228-20insGGGGGGGGGGGGGGGG		intron	N/A	ENSP00000497569.1
	DARS2	ENST00000648055.1		n.2140_2141insGGGGGGGGGGGGGGGG		non_coding_transcript_exon	Exon 2 of 3
	DARS2	ENST00000647645.1		c.228-21_228-20insGGGGGGGGGGGGGGGG		intron	N/A	ENSP00000497450.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome AF: 0.00000143 AC: 2 AN: 1401944 Hom.: 0 Cov.: 22 AF XY: 0.00000143 AC XY: 1 AN XY: 698270

African (AFR) AF: 0.00 AC: 0 AN: 32282

American (AMR) AF: 0.00 AC: 0 AN: 43874

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24638

East Asian (EAS) AF: 0.00 AC: 0 AN: 38084

South Asian (SAS) AF: 0.00 AC: 0 AN: 82006

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52158

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5542

European-Non Finnish (NFE) AF: 0.00000188 AC: 2 AN: 1065656

Other (OTH) AF: 0.00 AC: 0 AN: 57704

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs367543010; hg19: chr1-173797450;