11-24659986-G-T

Position:

• chr11-24659986-G-T

Variant summary

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

The NM_001009909.4(LUZP2):​c.63-69183G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,890 control chromosomes in the GnomAD database, including 17,951 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 0.48 (17951 hom., cov: 32)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LUZP2	NM_001009909.4	c.63-69183G>T		intron_variant		ENST00000336930.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LUZP2	ENST00000336930.11	c.63-69183G>T		intron_variant		1	NM_001009909.4	P1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72277 AN: 151772 Hom.: 17928 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.476 AC: 72349 AN: 151890 Hom.: 17951 Cov.: 32 AF XY: 0.473 AC XY: 35140 AN XY: 74228

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.431

Alfa AF: 0.428 Hom.: 19151

Bravo AF: 0.496

Asia WGS AF: 0.471 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.34

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: rs3923615; hg19: chr11-24681532;