dbSNP rs883524: LOXL2-AS1:n.871T>C (chr8-23337078-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 ENST00000519692.1(LOXL2-AS1):n.871T>C 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 0.164 in 152,182 control chromosomes in the GnomAD database, including 2,220 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 0.16 ( 2220 hom., cov: 32)

Exomes 𝑓: 0.21 ( 0 hom. )

Consequence

LOXL2-AS1
ENST00000519692.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.98

Publications

6 publications found

Variant links:

Genes affected

LOXL2-AS1 (HGNC:56648): (LOXL2 antisense RNA 1)

LOXL2-AS1 links:

LOXL2 (HGNC:6666): (lysyl oxidase like 2) This gene encodes a member of the lysyl oxidase gene family. The prototypic member of the family is essential to the biogenesis of connective tissue, encoding an extracellular copper-dependent amine oxidase that catalyses the first step in the formation of crosslinks in collagens and elastin. A highly conserved amino acid sequence at the C-terminus end appears to be sufficient for amine oxidase activity, suggesting that each family member may retain this function. The N-terminus is poorly conserved and may impart additional roles in developmental regulation, senescence, tumor suppression, cell growth control, and chemotaxis to each member of the family. [provided by RefSeq, Jul 2008]

LOXL2 links:

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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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOXL2	NM_002318.3 link	c.744-3455A>G		intron_variant	Intron 4 of 13	ENST00000389131.8	NP_002309.1	Q9Y4K0
LOXL2-AS1	NR_038323.1 link	n.871T>C		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LOXL2	ENST00000389131.8 link	c.744-3455A>G		intron_variant	Intron 4 of 13	1	NM_002318.3	ENSP00000373783.3		Q9Y4K0

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24906

AN:

152040

Hom.:

2219

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.0670

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.177

GnomAD4 exome

AF:

0.208

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.188

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.445

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.164

AC:

24907

AN:

152158

Hom.:

2220

Cov.:

AF XY:

0.166

AC XY:

12384

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.146

AC:

6065

AN:

41498

American (AMR)

AF:

0.206

AC:

3156

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

504

AN:

3466

East Asian (EAS)

AF:

0.0670

AC:

347

AN:

5180

South Asian (SAS)

AF:

0.330

AC:

1591

AN:

4822

European-Finnish (FIN)

AF:

0.128

AC:

1357

AN:

10598

Middle Eastern (MID)

AF:

0.240

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.166

AC:

11288

AN:

67992

Other (OTH)

AF:

0.179

AC:

377

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1062

2125

3187

4250

5312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.171

Hom.:

3269

Bravo

AF:

0.161

Asia WGS

AF:

0.201

AC:

699

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.30

(source)

DANN

Benign

0.73

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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rs883524

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over