chr15-73906472-T-G

Variant names:

• chr15-73906472-T-G
• rs4886467
• XM_011521281.4:c.979-3179T>G

Variant summary

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

The ENST00000804490.1(LOXL1-AS1):​n.380+5713A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,954 control chromosomes in the GnomAD database, including 29,041 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 0.61 (29041 hom., cov: 31)
• Consequence: LOXL1-AS1 ENST00000804490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 7 publications found

Genes affected

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]

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOXL1-AS1	ENST00000804490.1		n.380+5713A>C		intron	N/A
	LOXL1-AS1	ENST00000804491.1		n.430+5713A>C		intron	N/A
	LOXL1-AS1	ENST00000804492.1		n.455+5713A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93098 AN: 151836 Hom.: 29005 Cov.: 31

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.613 AC: 93187 AN: 151954 Hom.: 29041 Cov.: 31 AF XY: 0.617 AC XY: 45788 AN XY: 74270

African (AFR) AF: 0.642 AC: 26593 AN: 41410

American (AMR) AF: 0.579 AC: 8833 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1703 AN: 3468

East Asian (EAS) AF: 0.956 AC: 4943 AN: 5168

South Asian (SAS) AF: 0.690 AC: 3327 AN: 4822

European-Finnish (FIN) AF: 0.596 AC: 6298 AN: 10566

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39523 AN: 67960

Other (OTH) AF: 0.612 AC: 1292 AN: 2110

Alfa AF: 0.587 Hom.: 101823

Bravo AF: 0.612

Asia WGS AF: 0.820 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.087
DANN	Benign	0.54
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs4886467; hg19: chr15-74198813;