Variant 15-73952003-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005576.4(LOXL1):c.*166C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 450,848 control chromosomes in the GnomAD database, including 50,114 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 0.48 ( 18068 hom., cov: 33)

Exomes 𝑓: 0.46 ( 32046 hom. )

Consequence

LOXL1
NM_005576.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.830

Variant links:

Genes affected

LOXL1 (HGNC:6665): (lysyl oxidase like 1) This gene encodes a member of the lysyl oxidase family of proteins. The prototypic member of the family is essential to the biogenesis of connective tissue, encoding an extracellular copper-dependent amine oxidase that catalyzes the first step in the formation of crosslinks in collagen and elastin. The encoded preproprotein is proteolytically processed to generate the mature enzyme. A highly conserved amino acid sequence at the C-terminus end appears to be sufficient for amine oxidase activity, suggesting that each family member may retain this function. The N-terminus is poorly conserved and may impart additional roles in developmental regulation, senescence, tumor suppression, cell growth control, and chemotaxis to each member of the family. Mutations in this gene are associated with exfoliation syndrome. [provided by RefSeq, Jan 2016]

LOXL1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOXL1	NM_005576.4 linkuse as main transcript	c.*166C>T		3_prime_UTR_variant	7/7	ENST00000261921.8	NP_005567.2
LOXL1	XM_017022179.2 linkuse as main transcript	c.*166C>T		3_prime_UTR_variant	7/7		XP_016877668.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
LOXL1	ENST00000261921.8 linkuse as main transcript	c.*166C>T	3_prime_UTR_variant	7/7	1	NM_005576.4	ENSP00000261921	P1
LOXL1	ENST00000562548.1 linkuse as main transcript	n.976C>T	non_coding_transcript_exon_variant	3/3	2
LOXL1	ENST00000567675.1 linkuse as main transcript	n.327C>T	non_coding_transcript_exon_variant	3/3	3

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

73258

AN:

152008

Hom.:

18034

Cov.:

show subpopulations

Gnomad AFR

AF:

0.573

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.475

Gnomad ASJ

AF:

0.426

Gnomad EAS

AF:

0.601

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.478

GnomAD4 exome

AF:

0.458

AC:

136812

AN:

298722

Hom.:

32046

Cov.:

AF XY:

0.458

AC XY:

70451

AN XY:

153896

show subpopulations

Gnomad4 AFR exome

AF:

0.582

Gnomad4 AMR exome

AF:

0.481

Gnomad4 ASJ exome

AF:

0.437

Gnomad4 EAS exome

AF:

0.645

Gnomad4 SAS exome

AF:

0.574

Gnomad4 FIN exome

AF:

0.437

Gnomad4 NFE exome

AF:

0.426

Gnomad4 OTH exome

AF:

0.460

GnomAD4 genome

AF:

0.482

AC:

73357

AN:

152126

Hom.:

18068

Cov.:

AF XY:

0.486

AC XY:

36148

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.574

Gnomad4 AMR

AF:

0.476

Gnomad4 ASJ

AF:

0.426

Gnomad4 EAS

AF:

0.601

Gnomad4 SAS

AF:

0.583

Gnomad4 FIN

AF:

0.452

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.482

Alfa

AF:

0.431

Hom.:

19154

Bravo

AF:

0.487

Asia WGS

AF:

0.604

AC:

2102

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

2.4

DANN

Benign

0.90

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over