Variant 5-122077195-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001178102.2(LOX):c.-253G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,468,378 control chromosomes in the GnomAD database, including 19,374 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1694 hom., cov: 32)

Exomes 𝑓: 0.16 ( 17680 hom. )

Consequence

LOX
NM_001178102.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.145

Variant links:

Genes affected

LOX (HGNC:6664): (lysyl oxidase) This gene encodes a member of the lysyl oxidase family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate a regulatory propeptide and the mature enzyme. The copper-dependent amine oxidase activity of this enzyme functions in the crosslinking of collagens and elastin, while the propeptide may play a role in tumor suppression. In addition, defects in this gene have been linked with predisposition to thoracic aortic aneurysms and dissections. [provided by RefSeq, Jul 2016]

LOX links:

SRFBP1 (HGNC:26333): (serum response factor binding protein 1) Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA. Predicted to be located in perinuclear region of cytoplasm. Predicted to be part of 90S preribosome. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SRFBP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BP6

Variant 5-122077195-C-G is Benign according to our data. Variant chr5-122077195-C-G is described in ClinVar as [Benign]. Clinvar id is 1288647.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein	UniProt
LOX	NM_002317.7 linkuse as main transcript	c.631+160G>C	intron_variant		ENST00000231004.5	NP_002308.2	P28300D0PNI2
LOX	NM_001178102.2 linkuse as main transcript	c.-253G>C	5_prime_UTR_variant	1/6		NP_001171573.1	B7ZAJ4
SRFBP1	XM_017009111.3 linkuse as main transcript	c.*1870C>G	3_prime_UTR_variant	8/8		XP_016864600.2
LOX	NM_001317073.1 linkuse as main transcript	c.-255G>C	upstream_gene_variant			NP_001304002.1	B0AZT2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LOX	ENST00000231004.5 linkuse as main transcript	c.631+160G>C		intron_variant		1	NM_002317.7	ENSP00000231004.4		P28300

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21603

AN:

151942

Hom.:

1693

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0942

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.166

Gnomad EAS

AF:

0.146

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.166

GnomAD4 exome

AF:

0.162

AC:

213775

AN:

1316318

Hom.:

17680

Cov.:

AF XY:

0.162

AC XY:

104307

AN XY:

642000

show subpopulations

Gnomad4 AFR exome

AF:

0.0904

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.160

Gnomad4 EAS exome

AF:

0.128

Gnomad4 SAS exome

AF:

0.154

Gnomad4 FIN exome

AF:

0.130

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.163

GnomAD4 genome

AF:

0.142

AC:

21607

AN:

152060

Hom.:

1694

Cov.:

AF XY:

0.139

AC XY:

10357

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.0942

Gnomad4 AMR

AF:

0.163

Gnomad4 ASJ

AF:

0.166

Gnomad4 EAS

AF:

0.146

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.168

Gnomad4 OTH

AF:

0.164

Alfa

AF:

0.0749

Hom.:

Bravo

AF:

0.145

Asia WGS

AF:

0.108

AC:

376

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.85

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over