11-24771188-T-C

Position:

• chr11-24771188-T-C

Variant summary

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

The NM_001009909.4(LUZP2):​c.396+7880T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 150,686 control chromosomes in the GnomAD database, including 33,917 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 0.67 (33917 hom., cov: 28)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LUZP2	NM_001009909.4	c.396+7880T>C		intron_variant		ENST00000336930.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LUZP2	ENST00000336930.11	c.396+7880T>C		intron_variant		1	NM_001009909.4	P1

Frequencies

GnomAD3 genomes AF: 0.669 AC: 100725 AN: 150566 Hom.: 33880 Cov.: 28

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.669 AC: 100814 AN: 150686 Hom.: 33917 Cov.: 28 AF XY: 0.662 AC XY: 48677 AN XY: 73544

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.653

Alfa AF: 0.593 Hom.: 1798

Bravo AF: 0.667

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.49

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: rs2631407; hg19: chr11-24792734;