rs868675

Positions:

• chr1-119230973-T-C

Variant summary

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

The NR_125975.1(WARS2-AS1):​n.765-30474T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.45 in 152,002 control chromosomes in the GnomAD database, including 15,838 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 0.45 (15838 hom., cov: 32)
• Consequence: WARS2-AS1 NR_125975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

WARS2-AS1 (HGNC:40612): (WARS2 antisense RNA 1)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WARS2-AS1	NR_125975.1	n.765-30474T>C		intron_variant, non_coding_transcript_variant
WARS2-AS1	NR_125976.1	n.765-2485T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WARS2-AS1	ENST00000418015.1	n.431-30474T>C		intron_variant, non_coding_transcript_variant		2
	ENST00000655614.1	n.255-193A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68284 AN: 151884 Hom.: 15813 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.450 AC: 68358 AN: 152002 Hom.: 15838 Cov.: 32 AF XY: 0.444 AC XY: 33030 AN XY: 74310

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.455

Alfa AF: 0.467 Hom.: 20247

Bravo AF: 0.448

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs868675; hg19: chr1-119773596;