dbSNP rs10883597: LBX1-AS1:n.2478C>T (chr10-101239997-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000546988.3(LBX1-AS1):n.2478C>T 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 0.38 in 151,946 control chromosomes in the GnomAD database, including 11,223 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 0.38 ( 11223 hom., cov: 32)

Consequence

LBX1-AS1
ENST00000546988.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.102

Variant links:

Genes affected

LBX1-AS1 (HGNC:48678): (LBX1 antisense RNA 1)

LBX1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LBX1-AS1	ENST00000546988.3 link	n.2478C>T		non_coding_transcript_exon_variant	Exon 3 of 3	1
LBX1-AS1	ENST00000434878.1 link	n.110+1950C>T		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.380

AC:

57709

AN:

151828

Hom.:

11217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.329

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.541

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.381

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

GnomAD4 genome

AF:

0.380

AC:

57742

AN:

151946

Hom.:

11223

Cov.:

AF XY:

0.375

AC XY:

27866

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.349

Gnomad4 AMR

AF:

0.329

Gnomad4 ASJ

AF:

0.386

Gnomad4 EAS

AF:

0.542

Gnomad4 SAS

AF:

0.239

Gnomad4 FIN

AF:

0.381

Gnomad4 NFE

AF:

0.409

Gnomad4 OTH

AF:

0.381

Alfa

AF:

0.390

Hom.:

4121

Bravo

AF:

0.382

Asia WGS

AF:

0.353

AC:

1228

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.4

DANN

Benign

0.48

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