15-73903181-G-A

Variant names:

• chr15-73903181-G-A
• rs34894704
• ENST00000804490.1:n.381-3682C>T

Variant summary

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

The ENST00000804490.1(LOXL1-AS1):​n.381-3682C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,078 control chromosomes in the GnomAD database, including 4,448 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 0.22 (4448 hom., cov: 33)
• Consequence: LOXL1-AS1 ENST00000804490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 2 publications found

Genes affected

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

TBC1D21 (HGNC:28536): (TBC1 domain family member 21) Predicted to enable GTPase activator activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000804490.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOXL1-AS1	ENST00000804490.1		n.381-3682C>T		intron	N/A
	LOXL1-AS1	ENST00000804491.1		n.431-3682C>T		intron	N/A
	LOXL1-AS1	ENST00000804492.1		n.456-3682C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33031 AN: 151960 Hom.: 4445 Cov.: 33

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.234

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

GnomAD4 genome AF: 0.217 AC: 33046 AN: 152078 Hom.: 4448 Cov.: 33 AF XY: 0.221 AC XY: 16448 AN XY: 74332

African (AFR) AF: 0.130 AC: 5387 AN: 41490

American (AMR) AF: 0.248 AC: 3798 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3472

East Asian (EAS) AF: 0.683 AC: 3531 AN: 5170

South Asian (SAS) AF: 0.264 AC: 1273 AN: 4814

European-Finnish (FIN) AF: 0.214 AC: 2263 AN: 10562

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15387 AN: 67970

Other (OTH) AF: 0.237 AC: 500 AN: 2106

Alfa AF: 0.218 Hom.: 1341

Bravo AF: 0.220

Asia WGS AF: 0.399 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.49
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs34894704; hg19: chr15-74195522;