rs7524644

Variant names:

• chr1-119224060-C-T
• rs7524644
• ENST00000413531.5:n.431-9398C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000413531.5(WARS2-AS1):​n.431-9398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 152,262 control chromosomes in the GnomAD database, including 66,643 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 0.93 (66643 hom., cov: 32)
• Consequence: WARS2-AS1 ENST00000413531.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 1 publications found

Genes affected

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

ENSG00000227712 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.973 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WARS2-AS1	NR_125975.1		n.765-37387C>T		intron	N/A
	WARS2-AS1	NR_125976.1		n.765-9398C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	WARS2-AS1	ENST00000413531.5	TSL:1	n.431-9398C>T		intron	N/A
	WARS2-AS1	ENST00000418015.1	TSL:2	n.431-37387C>T		intron	N/A
	WARS2-AS1	ENST00000667138.1		n.703-12572C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.934 AC: 142104 AN: 152144 Hom.: 66605 Cov.: 32

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.966

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.947

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

GnomAD4 genome AF: 0.934 AC: 142191 AN: 152262 Hom.: 66643 Cov.: 32 AF XY: 0.933 AC XY: 69488 AN XY: 74460

African (AFR) AF: 0.857 AC: 35584 AN: 41524

American (AMR) AF: 0.966 AC: 14782 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3416 AN: 3472

East Asian (EAS) AF: 0.773 AC: 4003 AN: 5180

South Asian (SAS) AF: 0.922 AC: 4444 AN: 4822

European-Finnish (FIN) AF: 0.958 AC: 10163 AN: 10608

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.979 AC: 66621 AN: 68040

Other (OTH) AF: 0.940 AC: 1985 AN: 2112

Alfa AF: 0.963 Hom.: 280997

Bravo AF: 0.934

Asia WGS AF: 0.842 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	20
DANN	Benign	0.78
PhyloP100		1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7524644;

hg19: chr1-119766683;