Genetic Variant LBX1-AS1:n.420-1900T>C (chr10-101236039-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000546988.3(LBX1-AS1):n.420-1900T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 150,158 control chromosomes in the GnomAD database, including 23,208 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 0.55 ( 23196 hom., cov: 26)

Exomes 𝑓: 0.62 ( 12 hom. )

Consequence

LBX1-AS1
ENST00000546988.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.323

Publications

6 publications found

Variant links:

Genes affected

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

LBX1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LBX1-AS1	NR_029380.1 link	n.403-1900T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LBX1-AS1	ENST00000546988.3 link	n.420-1900T>C	intron_variant	Intron 2 of 2	1
LBX1-AS1	ENST00000454527.2 link	n.184-1900T>C	intron_variant	Intron 1 of 2	5
LBX1-AS1	ENST00000823572.1 link	n.274-1900T>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.548

AC:

82257

AN:

149996

Hom.:

23189

Cov.:

show subpopulations

Gnomad AFR

AF:

0.411

Gnomad AMI

AF:

0.730

Gnomad AMR

AF:

0.635

Gnomad ASJ

AF:

0.583

Gnomad EAS

AF:

0.603

Gnomad SAS

AF:

0.705

Gnomad FIN

AF:

0.665

Gnomad MID

AF:

0.640

Gnomad NFE

AF:

0.573

Gnomad OTH

AF:

0.576

GnomAD4 exome

AF:

0.619

AC:

AN:

Hom.:

Cov.:

AF XY:

0.559

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.607

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.700

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.548

AC:

82304

AN:

150116

Hom.:

23196

Cov.:

AF XY:

0.557

AC XY:

40820

AN XY:

73284

show subpopulations

African (AFR)

AF:

0.411

AC:

16746

AN:

40732

American (AMR)

AF:

0.635

AC:

9589

AN:

15100

Ashkenazi Jewish (ASJ)

AF:

0.583

AC:

2023

AN:

3468

East Asian (EAS)

AF:

0.602

AC:

3007

AN:

4994

South Asian (SAS)

AF:

0.705

AC:

3319

AN:

4708

European-Finnish (FIN)

AF:

0.665

AC:

6812

AN:

10248

Middle Eastern (MID)

AF:

0.633

AC:

186

AN:

294

European-Non Finnish (NFE)

AF:

0.573

AC:

38750

AN:

67576

Other (OTH)

AF:

0.579

AC:

1209

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1748

3495

5243

6990

8738

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.562

Hom.:

34903

Bravo

AF:

0.533

Asia WGS

AF:

0.648

AC:

2255

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.3

(source)

DANN

Benign

0.60

PhyloP100

0.32

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over