rs1386244

chr11-24784168-T-A

Variant summary

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

The NM_001009909.4(LUZP2):c.396+20860T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,644 control chromosomes in the GnomAD database, including 34,309 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 (34309 hom., cov: 31)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360

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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LUZP2	NM_001009909.4	c.396+20860T>A		intron_variant		ENST00000336930.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LUZP2	ENST00000336930.11	c.396+20860T>A		intron_variant		1	NM_001009909.4	P1

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101648 AN: 151526 Hom.: 34268 Cov.: 31

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.671 AC: 101743 AN: 151644 Hom.: 34309 Cov.: 31 AF XY: 0.664 AC XY: 49203 AN XY: 74110

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.650

Alfa AF: 0.684 Hom.: 4440

Bravo AF: 0.666

Asia WGS AF: 0.573 AC: 1992 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	8.1
Dann	Benign	0.77

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: rs1386244; hg19: chr11-24805714;