rs4886761

chr15-73923210-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040069.1(LOXL1-AS1):n.185-3172G>A variant causes a intron, non coding transcript 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 NR_040069.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOXL1-AS1	NR_040069.1	n.185-3172G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LOXL1-AS1	ENST00000685373.1	n.199-3172G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.0892

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.299

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4886761; hg19: chr15-74215551;