11-24589584-C-G

Position:

• chr11-24589584-C-G

Variant summary

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

The NM_001009909.4(LUZP2):​c.62+92279C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,094 control chromosomes in the GnomAD database, including 2,157 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 0.16 (2157 hom., cov: 33)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.62+92279C>G		intron_variant		ENST00000336930.11	NP_001009909.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.62+92279C>G		intron_variant		1	NM_001009909.4	ENSP00000336817	P1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24427 AN: 151974 Hom.: 2159 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.0368

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.161 AC: 24437 AN: 152094 Hom.: 2157 Cov.: 33 AF XY: 0.161 AC XY: 11994 AN XY: 74342

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.0867

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0797 Hom.: 112

Bravo AF: 0.161

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.66
DANN	Benign	0.55

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: rs12361953; hg19: chr11-24611130;