Variant chr1-119224060-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.28

Variant links:

Genes affected

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

WARS2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	UniProt
WARS2-AS1	NR_125975.1 linkuse as main transcript	n.765-37387C>T		intron_variant, non_coding_transcript_variant
WARS2-AS1	NR_125976.1 linkuse as main transcript	n.765-9398C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
WARS2-AS1	ENST00000413531.5 linkuse as main transcript	n.431-9398C>T	intron_variant, non_coding_transcript_variant	1
WARS2-AS1	ENST00000418015.1 linkuse as main transcript	n.431-37387C>T	intron_variant, non_coding_transcript_variant	2
WARS2-AS1	ENST00000667138.1 linkuse as main transcript	n.703-12572C>T	intron_variant, non_coding_transcript_variant
WARS2-AS1	ENST00000685192.2 linkuse as main transcript	n.652-9398C>T	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.934

AC:

142104

AN:

152144

Hom.:

66605

Cov.:

show subpopulations

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.:

AF XY:

0.933

AC XY:

69488

AN XY:

74460

show subpopulations

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

DANN

Benign

0.78

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over