11-24784168-T-A

Variant names:

• chr11-24784168-T-A
• rs1386244
• NM_001009909.4:c.396+20860T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.77).
• 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 rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.396+20860T>A		intron_variant	Intron 5 of 11	ENST00000336930.11	NP_001009909.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.396+20860T>A		intron_variant	Intron 5 of 11	1	NM_001009909.4	ENSP00000336817.6

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

African (AFR) AF: 0.706 AC: 29224 AN: 41392

American (AMR) AF: 0.572 AC: 8680 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2282 AN: 3464

East Asian (EAS) AF: 0.468 AC: 2404 AN: 5142

South Asian (SAS) AF: 0.642 AC: 3084 AN: 4800

European-Finnish (FIN) AF: 0.656 AC: 6927 AN: 10552

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47086 AN: 67802

Other (OTH) AF: 0.650 AC: 1372 AN: 2110

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
PhyloP100		0.36
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: rs1386244; hg19: chr11-24805714;