Variant 1-119140767-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000413531.5(WARS2-AS1):n.38G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 884,934 control chromosomes in the GnomAD database, including 33,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6798 hom., cov: 33)

Exomes 𝑓: 0.26 ( 26361 hom. )

Consequence

WARS2-AS1
ENST00000413531.5 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.74

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-119140767-G-A is Benign according to our data. Variant chr1-119140767-G-A is described in ClinVar as [Benign]. Clinvar id is 1178536.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
WARS2-AS1	NR_125974.1 link	n.372G>A	non_coding_transcript_exon_variant	Exon 1 of 4
WARS2-AS1	NR_125975.1 link	n.372G>A	non_coding_transcript_exon_variant	Exon 1 of 7
WARS2-AS1	NR_125976.1 link	n.372G>A	non_coding_transcript_exon_variant	Exon 1 of 5
WARS2-AS1	NR_125977.1 link	n.372G>A	non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
WARS2-AS1	ENST00000413531.5 link	n.38G>A	non_coding_transcript_exon_variant	Exon 1 of 5	1
WARS2-AS1	ENST00000425884.7 link	n.372G>A	non_coding_transcript_exon_variant	Exon 1 of 4	1
WARS2-AS1	ENST00000440150.5 link	n.343G>A	non_coding_transcript_exon_variant	Exon 1 of 4	1

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43766

AN:

152040

Hom.:

6789

Cov.:

show subpopulations

Gnomad AFR

AF:

0.392

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.0506

Gnomad SAS

AF:

0.282

Gnomad FIN

AF:

0.241

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.272

Gnomad OTH

AF:

0.265

GnomAD4 exome

AF:

0.259

AC:

190049

AN:

732776

Hom.:

26361

Cov.:

AF XY:

0.260

AC XY:

96195

AN XY:

370264

show subpopulations

Gnomad4 AFR exome

AF:

0.390

Gnomad4 AMR exome

AF:

0.146

Gnomad4 ASJ exome

AF:

0.270

Gnomad4 EAS exome

AF:

0.0444

Gnomad4 SAS exome

AF:

0.282

Gnomad4 FIN exome

AF:

0.243

Gnomad4 NFE exome

AF:

0.270

Gnomad4 OTH exome

AF:

0.259

GnomAD4 genome

AF:

0.288

AC:

43800

AN:

152158

Hom.:

6798

Cov.:

AF XY:

0.281

AC XY:

20907

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.392

Gnomad4 AMR

AF:

0.189

Gnomad4 ASJ

AF:

0.262

Gnomad4 EAS

AF:

0.0503

Gnomad4 SAS

AF:

0.283

Gnomad4 FIN

AF:

0.241

Gnomad4 NFE

AF:

0.272

Gnomad4 OTH

AF:

0.262

Alfa

AF:

0.0984

Hom.:

142

Bravo

AF:

0.284

Asia WGS

AF:

0.202

AC:

701

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

May 17, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.027

DANN

Benign

0.80

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over