rs34894704

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr15-73903181-G-A
• chr15-73903181-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBC1D21	XM_011521281.4	c.979-6470G>A		intron_variant	Intron 10 of 10		XP_011519583.1
TBC1D21	XM_011521283.3	c.979-4061G>A		intron_variant	Intron 10 of 10		XP_011519585.1
TBC1D21	XM_047432198.1	c.871-6470G>A		intron_variant	Intron 9 of 9		XP_047288154.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LOXL1-AS1	ENST00000804490.1	n.381-3682C>T		intron_variant	Intron 3 of 3
LOXL1-AS1	ENST00000804491.1	n.431-3682C>T		intron_variant	Intron 3 of 3
LOXL1-AS1	ENST00000804492.1	n.456-3682C>T		intron_variant	Intron 4 of 4

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 v4.3

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;