rs55736920

Variant names:

• chr15-73902673-C-T
• rs55736920
• XM_011521281.4:c.979-6978C>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.381-3174G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,236 control chromosomes in the GnomAD database, including 1,443 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 0.12 (1443 hom., cov: 32)
• Consequence: LOXL1-AS1 ENST00000804490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44
• Publications: 0 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 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.381-3174G>A		intron	N/A
	LOXL1-AS1	ENST00000804491.1		n.431-3174G>A		intron	N/A
	LOXL1-AS1	ENST00000804492.1		n.456-3174G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18444 AN: 152118 Hom.: 1444 Cov.: 32

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.0729

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.121 AC: 18441 AN: 152236 Hom.: 1443 Cov.: 32 AF XY: 0.118 AC XY: 8806 AN XY: 74430

African (AFR) AF: 0.0605 AC: 2513 AN: 41558

American (AMR) AF: 0.0809 AC: 1238 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 344 AN: 3470

East Asian (EAS) AF: 0.0174 AC: 90 AN: 5182

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1766 AN: 10606

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11826 AN: 67978

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.153 Hom.: 258

Bravo AF: 0.110

Asia WGS AF: 0.0540 AC: 187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs55736920;

hg19: chr15-74195014;