11-24649794-A-G

Variant names:

• chr11-24649794-A-G
• rs12362733
• NM_001009909.4:c.63-79375A>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.63-79375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,746 control chromosomes in the GnomAD database, including 1,935 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 0.14 (1935 hom., cov: 32)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001009909.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUZP2	NM_001009909.4	MANE Select	c.63-79375A>G		intron	N/A	NP_001009909.2
	LUZP2	NM_001252010.2		c.63-79375A>G		intron	N/A	NP_001238939.1
	LUZP2	NM_001252008.2		c.-192-79379A>G		intron	N/A	NP_001238937.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUZP2	ENST00000336930.11	TSL:1 MANE Select	c.63-79375A>G		intron	N/A	ENSP00000336817.6
	LUZP2	ENST00000533227.5	TSL:1	c.-192-79379A>G		intron	N/A	ENSP00000432952.1
	LUZP2	ENST00000405855.6	TSL:1	n.168-79375A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21473 AN: 151628 Hom.: 1935 Cov.: 32

Gnomad AFR AF: 0.0418

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.141 AC: 21466 AN: 151746 Hom.: 1935 Cov.: 32 AF XY: 0.139 AC XY: 10346 AN XY: 74166

African (AFR) AF: 0.0417 AC: 1728 AN: 41438

American (AMR) AF: 0.214 AC: 3259 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3468

East Asian (EAS) AF: 0.0466 AC: 240 AN: 5154

South Asian (SAS) AF: 0.103 AC: 498 AN: 4812

European-Finnish (FIN) AF: 0.163 AC: 1717 AN: 10532

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13069 AN: 67814

Other (OTH) AF: 0.150 AC: 316 AN: 2108

Alfa AF: 0.182 Hom.: 2429

Bravo AF: 0.142

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.71
PhyloP100		-0.72
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: rs12362733; hg19: chr11-24671340;