rs10834489

Variant names:

• chr11-24816255-C-T
• rs10834489
• NM_001009909.4:c.396+52947C>T

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+52947C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,588 control chromosomes in the GnomAD database, including 10,542 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 0.35 (10542 hom., cov: 30)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.396+52947C>T		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+52947C>T		intron_variant	Intron 5 of 11	1	NM_001009909.4	ENSP00000336817.6

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53248 AN: 151472 Hom.: 10540 Cov.: 30

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.351 AC: 53268 AN: 151588 Hom.: 10542 Cov.: 30 AF XY: 0.355 AC XY: 26312 AN XY: 74022

African (AFR) AF: 0.166 AC: 6839 AN: 41302

American (AMR) AF: 0.384 AC: 5848 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3236 AN: 5130

South Asian (SAS) AF: 0.406 AC: 1954 AN: 4816

European-Finnish (FIN) AF: 0.408 AC: 4267 AN: 10462

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.418 AC: 28406 AN: 67888

Other (OTH) AF: 0.365 AC: 766 AN: 2100

Alfa AF: 0.394 Hom.: 20262

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.4
DANN	Benign	0.46
PhyloP100		1.0
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: rs10834489; hg19: chr11-24837801;