ENST00000413531.5:n.431-2485T>C

Variant names:

• chr1-119230973-T-C
• rs868675
• ENST00000413531.5:n.431-2485T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000413531.5(WARS2-AS1):​n.431-2485T>C variant causes a intron 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 ENST00000413531.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 2 publications found

Genes affected

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

ENSG00000227712 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413531.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WARS2-AS1	NR_125975.1		n.765-30474T>C		intron	N/A
	WARS2-AS1	NR_125976.1		n.765-2485T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WARS2-AS1	ENST00000413531.5	TSL:1	n.431-2485T>C		intron	N/A
	WARS2-AS1	ENST00000418015.1	TSL:2	n.431-30474T>C		intron	N/A
	ENSG00000227712	ENST00000655614.1		n.255-193A>G		intron	N/A

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

African (AFR) AF: 0.500 AC: 20736 AN: 41466

American (AMR) AF: 0.370 AC: 5646 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1858 AN: 3468

East Asian (EAS) AF: 0.147 AC: 762 AN: 5176

South Asian (SAS) AF: 0.538 AC: 2587 AN: 4812

European-Finnish (FIN) AF: 0.351 AC: 3705 AN: 10558

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.463 AC: 31459 AN: 67954

Other (OTH) AF: 0.455 AC: 962 AN: 2112

Alfa AF: 0.466 Hom.: 23172

Bravo AF: 0.448

Asia WGS AF: 0.394 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.46
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs868675; hg19: chr1-119773596;