rs1596854

Variant names:

• chr11-25042751-A-G
• rs1596854
• NM_001009909.4:c.766-7287A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009909.4(LUZP2):​c.766-7287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 151,978 control chromosomes in the GnomAD database, including 17,022 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 0.47 (17022 hom., cov: 31)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969
• Publications: 4 publications found

Genes affected

LUZP2 (HGNC:23206): (leucine zipper protein 2) This gene encodes a leucine zipper protein. This protein is deleted in some patients with Wilms tumor-Aniridia-Genitourinary anomalies-mental Retardation (WAGR) syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.766-7287A>G		intron_variant	Intron 9 of 11	ENST00000336930.11	NP_001009909.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.766-7287A>G		intron_variant	Intron 9 of 11	1	NM_001009909.4	ENSP00000336817.6
LUZP2	ENST00000533227.5	c.508-7287A>G		intron_variant	Intron 9 of 11	1		ENSP00000432952.1
LUZP2	ENST00000620308.1	c.508-7287A>G		intron_variant	Intron 8 of 10	5		ENSP00000480441.1

Frequencies

GnomAD3 genomes AF: 0.466 AC: 70828 AN: 151860 Hom.: 17014 Cov.: 31

Gnomad AFR AF: 0.443

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.0852

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.466 AC: 70874 AN: 151978 Hom.: 17022 Cov.: 31 AF XY: 0.462 AC XY: 34303 AN XY: 74250

African (AFR) AF: 0.443 AC: 18381 AN: 41458

American (AMR) AF: 0.456 AC: 6968 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3468

East Asian (EAS) AF: 0.0850 AC: 437 AN: 5140

South Asian (SAS) AF: 0.455 AC: 2195 AN: 4820

European-Finnish (FIN) AF: 0.480 AC: 5058 AN: 10540

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34534 AN: 67966

Other (OTH) AF: 0.470 AC: 991 AN: 2110

Alfa AF: 0.501 Hom.: 23330

Bravo AF: 0.467

Asia WGS AF: 0.304 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.71
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1596854; hg19: chr11-25064297;