11-25078236-T-G

Position:

• chr11-25078236-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009909.4(LUZP2):​c.937-318T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,118 control chromosomes in the GnomAD database, including 11,716 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 0.36 (11716 hom., cov: 33)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.937-318T>G		intron_variant		ENST00000336930.11	NP_001009909.2
LUZP2	NM_001252010.2	c.811-318T>G		intron_variant			NP_001238939.1
LUZP2	NM_001252008.2	c.679-318T>G		intron_variant			NP_001238937.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.937-318T>G		intron_variant		1	NM_001009909.4	ENSP00000336817.6
LUZP2	ENST00000533227.5	c.679-318T>G		intron_variant		1		ENSP00000432952.1
LUZP2	ENST00000620308.1	c.679-318T>G		intron_variant		5		ENSP00000480441.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54347 AN: 152000 Hom.: 11708 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.357 AC: 54368 AN: 152118 Hom.: 11716 Cov.: 33 AF XY: 0.367 AC XY: 27295 AN XY: 74340

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.383

Alfa AF: 0.376 Hom.: 1485

Bravo AF: 0.343

Asia WGS AF: 0.574 AC: 1996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.76

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

Other links and lift over

dbSNP: rs10500993; hg19: chr11-25099782;