1-150487651-T-TCTAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_025150.5(TARS2):c.66+136_66+139dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00387 in 1,320,192 control chromosomes in the GnomAD database, including 127 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.017 (74 hom., cov: 32)
  • Exomes 𝑓: 0.0022 (53 hom.)
• Consequence: TARS2 NM_025150.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.24

Genes affected

TARS2 (HGNC:30740): (threonyl-tRNA synthetase 2, mitochondrial) This gene encodes a member of the class-II aminoacyl-tRNA synthetase family. The encoded protein is a mitochondrial aminoacyl-tRNA synthetase. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 4. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-150487651-T-TCTAA is Benign according to our data. Variant chr1-150487651-T-TCTAA is described in ClinVar as [Benign]. Clinvar id is 1258473.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TARS2	NM_025150.5	c.66+136_66+139dup		intron_variant		ENST00000369064.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TARS2	ENST00000369064.8	c.66+136_66+139dup		intron_variant		1	NM_025150.5	P1

Frequencies

GnomAD3 genomes AF: 0.0169 AC: 2576 AN: 152152 Hom.: 75 Cov.: 32

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00936

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000705

Gnomad OTH AF: 0.0143

GnomAD4 exome AF: 0.00216 AC: 2519 AN: 1167922 Hom.: 53 AF XY: 0.00198 AC XY: 1152 AN XY: 581676

Gnomad4 AFR exome AF: 0.0564

Gnomad4 AMR exome AF: 0.00643

Gnomad4 ASJ exome AF: 0.00558

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000171

Gnomad4 FIN exome AF: 0.0000208

Gnomad4 NFE exome AF: 0.000525

Gnomad4 OTH exome AF: 0.00485

GnomAD4 genome AF: 0.0170 AC: 2585 AN: 152270 Hom.: 74 Cov.: 32 AF XY: 0.0163 AC XY: 1210 AN XY: 74452

Gnomad4 AFR AF: 0.0565

Gnomad4 AMR AF: 0.00935

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000706

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0106 Hom.: 5

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 04, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs201661242; hg19: chr1-150460127;