chr15-73919207-C-T

Position:

• chr15-73919207-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.440G>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 NR_040069.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOXL1-AS1	NR_040069.1	n.440G>A		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LOXL1-AS1	ENST00000685373.1	n.399+631G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.375

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

Gnomad4 AFR AF: 0.811

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.646

Alfa AF: 0.595 Hom.: 55203

Bravo AF: 0.663

Asia WGS AF: 0.655 AC: 2283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4461027; hg19: chr15-74211548;