1-119224060-C-T

Position:

• chr1-119224060-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_125975.1(WARS2-AS1):​n.765-37387C>T 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 0.934 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 NR_125975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
WARS2-AS1	NR_125975.1	n.765-37387C>T		intron_variant, non_coding_transcript_variant
WARS2-AS1	NR_125976.1	n.765-9398C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
WARS2-AS1	ENST00000413531.5	n.431-9398C>T		intron_variant, non_coding_transcript_variant		1
WARS2-AS1	ENST00000418015.1	n.431-37387C>T		intron_variant, non_coding_transcript_variant		2
WARS2-AS1	ENST00000667138.1	n.703-12572C>T		intron_variant, non_coding_transcript_variant
WARS2-AS1	ENST00000685192.2	n.652-9398C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.966

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.773

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.940

Alfa AF: 0.970 Hom.: 120033

Bravo AF: 0.934

Asia WGS AF: 0.842 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7524644; hg19: chr1-119766683;