15-73919207-C-T

Variant names:

• chr15-73919207-C-T
• rs4461027
• ENST00000562130.5:n.481G>A

Variant summary

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

The ENST00000562965.1(LOXL1-AS1):​n.1016G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,048 control chromosomes in the GnomAD database, including 33,400 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 0.65 (33400 hom., cov: 32)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: LOXL1-AS1 ENST00000562965.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 22 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562965.1. 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.747G>A		non_coding_transcript_exon	Exon 4 of 4
	LOXL1-AS1	NR_040067.1		n.625G>A		non_coding_transcript_exon	Exon 4 of 4
	LOXL1-AS1	NR_040068.1		n.562G>A		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOXL1-AS1	ENST00000562130.5	TSL:4	n.481G>A		non_coding_transcript_exon	Exon 3 of 3
	LOXL1-AS1	ENST00000562739.6	TSL:4	n.422G>A		non_coding_transcript_exon	Exon 3 of 3
	LOXL1-AS1	ENST00000562965.1	TSL:2	n.1016G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99357 AN: 151920 Hom.: 33345 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.644

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.654 AC: 99474 AN: 152038 Hom.: 33400 Cov.: 32 AF XY: 0.655 AC XY: 48669 AN XY: 74318

African (AFR) AF: 0.811 AC: 33635 AN: 41480

American (AMR) AF: 0.611 AC: 9341 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3472

East Asian (EAS) AF: 0.679 AC: 3507 AN: 5168

South Asian (SAS) AF: 0.698 AC: 3370 AN: 4826

European-Finnish (FIN) AF: 0.552 AC: 5822 AN: 10542

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39906 AN: 67956

Other (OTH) AF: 0.646 AC: 1366 AN: 2114

Alfa AF: 0.608 Hom.: 124618

Bravo AF: 0.663

Asia WGS AF: 0.655 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4461027; hg19: chr15-74211548;