rs9262288

chr6-30917862-A-Gchr6-30917862-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020442.6(VARS2):c.985+56A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 1,524,872 control chromosomes in the GnomAD database, including 88,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.28 (6832 hom., cov: 32)
  • Exomes 𝑓: 0.34 (81624 hom.)
• Consequence: VARS2 NM_020442.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.70

Genes affected

VARS2 (HGNC:21642): (valyl-tRNA synthetase 2, mitochondrial) This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP6: Variant 6-30917862-A-G is Benign according to our data. Variant chr6-30917862-A-G is described in ClinVar as [Benign]. Clinvar id is 1229689.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VARS2	NM_020442.6	c.985+56A>G		intron_variant		ENST00000676266.1
VARS2	NM_001167733.3	c.565+56A>G		intron_variant
VARS2	NM_001167734.2	c.1075+56A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VARS2	ENST00000676266.1	c.985+56A>G		intron_variant			NM_020442.6	P3

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42546 AN: 151902 Hom.: 6835 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.282

GnomAD4 exome AF: 0.340 AC: 466568 AN: 1372852 Hom.: 81624 AF XY: 0.339 AC XY: 230198 AN XY: 678684

Gnomad4 AFR exome AF: 0.116

Gnomad4 AMR exome AF: 0.224

Gnomad4 ASJ exome AF: 0.375

Gnomad4 EAS exome AF: 0.235

Gnomad4 SAS exome AF: 0.276

Gnomad4 FIN exome AF: 0.384

Gnomad4 NFE exome AF: 0.357

Gnomad4 OTH exome AF: 0.309

GnomAD4 genome AF: 0.280 AC: 42556 AN: 152020 Hom.: 6832 Cov.: 32 AF XY: 0.281 AC XY: 20883 AN XY: 74302

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.253

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.279

Alfa AF: 0.344 Hom.: 6019

Bravo AF: 0.263

Asia WGS AF: 0.208 AC: 726 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

Jun 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.043
Dann	Benign	0.51
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs9262288; hg19: chr6-30885639; COSMIC: COSV52558958; COSMIC: COSV52558958;