Variant chr22-20990595-C-T 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+70C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 1,476,362 control chromosomes in the GnomAD database, including 84,127 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.27 ( 6511 hom., cov: 33)

Exomes 𝑓: 0.33 ( 77616 hom. )

Consequence

LZTR1
NM_006767.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.79

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:

ENSG00000285314 (HGNC:):

ENSG00000285314 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=-0.87).

BP6

Variant 22-20990595-C-T is Benign according to our data. Variant chr22-20990595-C-T is described in ClinVar as [Benign]. Clinvar id is 561411.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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+70C>T		intron_variant		ENST00000646124.2	NP_006758.2	Q8N653A0A384NL67

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LZTR1	ENST00000646124.2 linkuse as main transcript	c.791+70C>T		intron_variant			NM_006767.4	ENSP00000496779.1		Q8N653

Frequencies

GnomAD3 genomes

AF:

0.268

AC:

40792

AN:

152030

Hom.:

6500

Cov.:

show subpopulations

Gnomad AFR

AF:

0.131

Gnomad AMI

AF:

0.418

Gnomad AMR

AF:

0.377

Gnomad ASJ

AF:

0.383

Gnomad EAS

AF:

0.0645

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.326

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.330

GnomAD4 exome

AF:

0.332

AC:

439618

AN:

1324214

Hom.:

77616

Cov.:

AF XY:

0.328

AC XY:

214643

AN XY:

654534

show subpopulations

Gnomad4 AFR exome

AF:

0.122

Gnomad4 AMR exome

AF:

0.401

Gnomad4 ASJ exome

AF:

0.391

Gnomad4 EAS exome

AF:

0.0834

Gnomad4 SAS exome

AF:

0.155

Gnomad4 FIN exome

AF:

0.235

Gnomad4 NFE exome

AF:

0.362

Gnomad4 OTH exome

AF:

0.319

GnomAD4 genome

AF:

0.268

AC:

40807

AN:

152148

Hom.:

6511

Cov.:

AF XY:

0.261

AC XY:

19404

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.131

Gnomad4 AMR

AF:

0.378

Gnomad4 ASJ

AF:

0.383

Gnomad4 EAS

AF:

0.0643

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.327

Alfa

AF:

0.331

Hom.:

12555

Bravo

AF:

0.282

Asia WGS

AF:

0.113

AC:

393

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

-0.87

CADD

Benign

0.21

DANN

Benign

0.73

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.0

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