rs8026259

Variant names:

• chr15-73924418-T-C
• rs8026259
• ENST00000562130.5:n.103+1822A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562130.5(LOXL1-AS1):​n.103+1822A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,090 control chromosomes in the GnomAD database, including 2,344 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 (2344 hom., cov: 32)
• Consequence: LOXL1-AS1 ENST00000562130.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.79
• Publications: 1 publications found

Genes affected

LOXL1-AS1 (HGNC:44169): (LOXL1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562130.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOXL1-AS1	NR_040066.1		n.369+852A>G		intron	N/A
	LOXL1-AS1	NR_040067.1		n.369+852A>G		intron	N/A
	LOXL1-AS1	NR_040068.1		n.184+3647A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOXL1-AS1	ENST00000562130.5	TSL:4	n.103+1822A>G		intron	N/A
	LOXL1-AS1	ENST00000562739.6	TSL:4	n.44+3236A>G		intron	N/A
	LOXL1-AS1	ENST00000562965.1	TSL:2	n.184+3359A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24377 AN: 151972 Hom.: 2348 Cov.: 32

Gnomad AFR AF: 0.0691

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0232

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.160 AC: 24374 AN: 152090 Hom.: 2344 Cov.: 32 AF XY: 0.163 AC XY: 12135 AN XY: 74348

African (AFR) AF: 0.0691 AC: 2868 AN: 41512

American (AMR) AF: 0.214 AC: 3264 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 751 AN: 3472

East Asian (EAS) AF: 0.0235 AC: 121 AN: 5152

South Asian (SAS) AF: 0.248 AC: 1194 AN: 4816

European-Finnish (FIN) AF: 0.182 AC: 1933 AN: 10594

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13720 AN: 67954

Other (OTH) AF: 0.163 AC: 344 AN: 2108

Alfa AF: 0.181 Hom.: 4101

Bravo AF: 0.152

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	18
DANN	Benign	0.81
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs8026259; hg19: chr15-74216759;