15-73912569-G-T

Variant names:

• chr15-73912569-G-T
• rs4558370
• ENST00000565689.5:n.139-266C>A

Variant summary

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

The ENST00000568229.5(LOXL1-AS1):​n.294-266C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,092 control chromosomes in the GnomAD database, including 2,890 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 0.19 (2890 hom., cov: 33)
• Consequence: LOXL1-AS1 ENST00000568229.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LOXL1-AS1	ENST00000565689.5	n.139-266C>A		intron_variant	Intron 2 of 3	3
LOXL1-AS1	ENST00000568087.5	n.368-266C>A		intron_variant	Intron 2 of 3	4
LOXL1-AS1	ENST00000568229.5	n.294-266C>A		intron_variant	Intron 2 of 3	2
LOXL1-AS1	ENST00000685373.1	n.400-266C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28280 AN: 151974 Hom.: 2876 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0543

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.186 AC: 28337 AN: 152092 Hom.: 2890 Cov.: 33 AF XY: 0.186 AC XY: 13851 AN XY: 74354

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0542

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.184

Alfa AF: 0.133 Hom.: 433

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4558370; hg19: chr15-74204910;