1-150494892-C-T

Position:

• chr1-150494892-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025150.5(TARS2):​c.775-1590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,240 control chromosomes in the GnomAD database, including 25,790 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (25790 hom., cov: 30)
• Consequence: TARS2 NM_025150.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TARS2	NM_025150.5	c.775-1590C>T		intron_variant		ENST00000369064.8	NP_079426.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TARS2	ENST00000369064.8	c.775-1590C>T		intron_variant		1	NM_025150.5	ENSP00000358060	P1

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87634 AN: 151122 Hom.: 25769 Cov.: 30

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.557

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.580 AC: 87694 AN: 151240 Hom.: 25790 Cov.: 30 AF XY: 0.573 AC XY: 42353 AN XY: 73868

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.555

Alfa AF: 0.600 Hom.: 3372

Bravo AF: 0.570

Asia WGS AF: 0.424 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11205384; hg19: chr1-150467368;