chr3-45391483-C-A

Position:

• chr3-45391483-C-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_015340.4(LARS2):​c.-87-100C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0059 (0 hom., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: LARS2 NM_015340.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.608

Genes affected

LARS2 (HGNC:17095): (leucyl-tRNA synthetase 2, mitochondrial) This gene encodes a class 1 aminoacyl-tRNA synthetase, mitochondrial leucyl-tRNA synthetase. Each of the twenty aminoacyl-tRNA synthetases catalyzes the aminoacylation of a specific tRNA or tRNA isoaccepting family with the cognate amino acid. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 3-45391483-C-A is Benign according to our data. Variant chr3-45391483-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1196616.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LARS2	NM_015340.4	c.-87-100C>A		intron_variant		ENST00000645846.2	NP_056155.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LARS2	ENST00000645846.2	c.-87-100C>A		intron_variant			NM_015340.4	ENSP00000495093	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 566 AN: 96684 Hom.: 0 Cov.: 22 FAILED QC

Gnomad AFR AF: 0.00709

Gnomad AMI AF: 0.00172

Gnomad AMR AF: 0.00604

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00550

Gnomad SAS AF: 0.00378

Gnomad FIN AF: 0.0147

Gnomad MID AF: 0.0103

Gnomad NFE AF: 0.00473

Gnomad OTH AF: 0.00467

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00586 AC: 567 AN: 96718 Hom.: 0 Cov.: 22 AF XY: 0.00632 AC XY: 289 AN XY: 45704

Gnomad4 AFR AF: 0.00711

Gnomad4 AMR AF: 0.00604

Gnomad4 ASJ AF: 0.00259

Gnomad4 EAS AF: 0.00552

Gnomad4 SAS AF: 0.00381

Gnomad4 FIN AF: 0.0147

Gnomad4 NFE AF: 0.00473

Gnomad4 OTH AF: 0.00460

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 28, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.27
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: rs967355397; hg19: chr3-45432975;