11-24657273-T-G

Variant names:

• chr11-24657273-T-G
• rs4561213
• NM_001009909.4:c.63-71896T>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.63-71896T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 151,876 control chromosomes in the GnomAD database, including 24,319 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 0.56 (24319 hom., cov: 32)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 9 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.63-71896T>G		intron_variant	Intron 1 of 11	ENST00000336930.11	NP_001009909.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.63-71896T>G		intron_variant	Intron 1 of 11	1	NM_001009909.4	ENSP00000336817.6

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85268 AN: 151758 Hom.: 24284 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.577

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.562 AC: 85355 AN: 151876 Hom.: 24319 Cov.: 32 AF XY: 0.558 AC XY: 41391 AN XY: 74202

African (AFR) AF: 0.634 AC: 26256 AN: 41404

American (AMR) AF: 0.615 AC: 9380 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2291 AN: 5142

South Asian (SAS) AF: 0.501 AC: 2415 AN: 4820

European-Finnish (FIN) AF: 0.473 AC: 4983 AN: 10532

Middle Eastern (MID) AF: 0.576 AC: 167 AN: 290

European-Non Finnish (NFE) AF: 0.535 AC: 36320 AN: 67946

Other (OTH) AF: 0.531 AC: 1120 AN: 2110

Alfa AF: 0.546 Hom.: 42559

Bravo AF: 0.580

Asia WGS AF: 0.513 AC: 1786 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.71
PhyloP100		0.20
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: rs4561213; hg19: chr11-24678819;