Variant rs178290 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006767.4(LZTR1):c.791+91A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 1,359,724 control chromosomes in the GnomAD database, including 389,877 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.74 ( 41671 hom., cov: 33)

Exomes 𝑓: 0.76 ( 348206 hom. )

Consequence

LZTR1
NM_006767.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.904

Variant links:

Genes affected

LZTR1 (HGNC:6742): (leucine zipper like post translational regulator 1) This gene encodes a member of the BTB-kelch superfamily. Initially described as a putative transcriptional regulator based on weak homology to members of the basic leucine zipper-like family, the encoded protein subsequently has been shown to localize exclusively to the Golgi network where it may help stabilize the Gogli complex. Deletion of this gene may be associated with DiGeorge syndrome. [provided by RefSeq, Jul 2008]

LZTR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 22-20990616-A-G is Benign according to our data. Variant chr22-20990616-A-G is described in ClinVar as [Benign]. Clinvar id is 561412.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LZTR1	NM_006767.4 linkuse as main transcript	c.791+91A>G		intron_variant		ENST00000646124.2	NP_006758.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LZTR1	ENST00000646124.2 linkuse as main transcript	c.791+91A>G		intron_variant			NM_006767.4	ENSP00000496779	P1

Frequencies

GnomAD3 genomes

AF:

0.738

AC:

112158

AN:

152012

Hom.:

41636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.702

Gnomad AMI

AF:

0.749

Gnomad AMR

AF:

0.815

Gnomad ASJ

AF:

0.738

Gnomad EAS

AF:

0.758

Gnomad SAS

AF:

0.607

Gnomad FIN

AF:

0.682

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.758

Gnomad OTH

AF:

0.756

GnomAD4 exome

AF:

0.758

AC:

915037

AN:

1207594

Hom.:

348206

Cov.:

AF XY:

0.753

AC XY:

452278

AN XY:

600566

show subpopulations

Gnomad4 AFR exome

AF:

0.691

Gnomad4 AMR exome

AF:

0.870

Gnomad4 ASJ exome

AF:

0.745

Gnomad4 EAS exome

AF:

0.781

Gnomad4 SAS exome

AF:

0.610

Gnomad4 FIN exome

AF:

0.696

Gnomad4 NFE exome

AF:

0.770

Gnomad4 OTH exome

AF:

0.745

GnomAD4 genome

AF:

0.738

AC:

112244

AN:

152130

Hom.:

41671

Cov.:

AF XY:

0.735

AC XY:

54666

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.702

Gnomad4 AMR

AF:

0.816

Gnomad4 ASJ

AF:

0.738

Gnomad4 EAS

AF:

0.758

Gnomad4 SAS

AF:

0.608

Gnomad4 FIN

AF:

0.682

Gnomad4 NFE

AF:

0.758

Gnomad4 OTH

AF:

0.754

Alfa

AF:

0.745

Hom.:

8602

Bravo

AF:

0.754

Asia WGS

AF:

0.680

AC:

2363

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.3

DANN

Benign

0.32

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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