rs4886761

Variant names:

• chr15-73923210-C-T
• rs4886761
• ENST00000562130.5:n.103+3030G>A

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+3030G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,168 control chromosomes in the GnomAD database, including 8,076 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 0.30 (8076 hom., cov: 33)
• Consequence: LOXL1-AS1 ENST00000562130.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 8 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOXL1-AS1	NR_040066.1	n.369+2060G>A		intron_variant	Intron 2 of 3
LOXL1-AS1	NR_040067.1	n.369+2060G>A		intron_variant	Intron 2 of 3
LOXL1-AS1	NR_040068.1	n.185-3172G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LOXL1-AS1	ENST00000562130.5	n.103+3030G>A		intron_variant	Intron 1 of 2	4
LOXL1-AS1	ENST00000562739.6	n.45-3172G>A		intron_variant	Intron 1 of 2	4
LOXL1-AS1	ENST00000562965.1	n.185-3172G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45727 AN: 152048 Hom.: 8074 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.301 AC: 45742 AN: 152168 Hom.: 8076 Cov.: 33 AF XY: 0.300 AC XY: 22292 AN XY: 74398

African (AFR) AF: 0.136 AC: 5653 AN: 41534

American (AMR) AF: 0.356 AC: 5451 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1304 AN: 3470

East Asian (EAS) AF: 0.0892 AC: 462 AN: 5178

South Asian (SAS) AF: 0.183 AC: 881 AN: 4822

European-Finnish (FIN) AF: 0.433 AC: 4584 AN: 10598

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26269 AN: 67958

Other (OTH) AF: 0.299 AC: 631 AN: 2112

Alfa AF: 0.357 Hom.: 1375

Bravo AF: 0.289

Asia WGS AF: 0.151 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.54
DANN	Benign	0.32
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4886761; hg19: chr15-74215551;