Variant chr5-122066902-C-T 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_002317.7(LOX):c.1248-153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,018 control chromosomes in the GnomAD database, including 6,710 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 6710 hom., cov: 32)

Consequence

LOX
NM_002317.7 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.480

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=-0.84).

BP6

Variant 5-122066902-C-T is Benign according to our data. Variant chr5-122066902-C-T is described in ClinVar as [Benign]. Clinvar id is 1277270.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
LOX	NM_002317.7 linkuse as main transcript	c.1248-153G>A	intron_variant	ENST00000231004.5
LOX	NM_001178102.2 linkuse as main transcript	c.558-153G>A	intron_variant
LOX	NM_001317073.1 linkuse as main transcript	c.357-153G>A	intron_variant
SRFBP1	XM_017009111.3 linkuse as main transcript	c.1106-8413C>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LOX	ENST00000231004.5 linkuse as main transcript	c.1248-153G>A		intron_variant		1	NM_002317.7	P1

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39738

AN:

151900

Hom.:

6672

Cov.:

show subpopulations

Gnomad AFR

AF:

0.481

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.190

Gnomad ASJ

AF:

0.197

Gnomad EAS

AF:

0.0895

Gnomad SAS

AF:

0.181

Gnomad FIN

AF:

0.180

Gnomad MID

AF:

0.156

Gnomad NFE

AF:

0.183

Gnomad OTH

AF:

0.243

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

GnomAD4 genome

AF:

0.262

AC:

39826

AN:

152018

Hom.:

6710

Cov.:

AF XY:

0.257

AC XY:

19084

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.482

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.197

Gnomad4 EAS

AF:

0.0901

Gnomad4 SAS

AF:

0.181

Gnomad4 FIN

AF:

0.180

Gnomad4 NFE

AF:

0.183

Gnomad4 OTH

AF:

0.241

Alfa

AF:

0.195

Hom.:

3316

Bravo

AF:

0.272

Asia WGS

AF:

0.142

AC:

494

AN:

3478

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

Sep 11, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.43

DANN

Benign

0.22

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over