ENST00000565689.6:n.471-266C>A

Variant names:

• chr15-73912569-G-T
• rs4558370
• ENST00000565689.6:n.471-266C>A

Variant summary

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

The ENST00000565689.6(LOXL1-AS1):​n.471-266C>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 ENST00000565689.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565689.6. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOXL1-AS1	ENST00000565689.6	TSL:3	n.471-266C>A		intron	N/A
	LOXL1-AS1	ENST00000568087.5	TSL:4	n.368-266C>A		intron	N/A
	LOXL1-AS1	ENST00000568229.6	TSL:2	n.299-266C>A		intron	N/A

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

African (AFR) AF: 0.242 AC: 10022 AN: 41468

American (AMR) AF: 0.207 AC: 3162 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5164

South Asian (SAS) AF: 0.208 AC: 1005 AN: 4826

European-Finnish (FIN) AF: 0.185 AC: 1956 AN: 10562

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10742 AN: 67994

Other (OTH) AF: 0.184 AC: 389 AN: 2114

Alfa AF: 0.133 Hom.: 433

Bravo AF: 0.189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.67
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs4558370; hg19: chr15-74204910;