11-25078236-T-G

Variant names:

• chr11-25078236-T-G
• rs10500993
• NM_001009909.4:c.937-318T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009909.4(LUZP2):​c.937-318T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,118 control chromosomes in the GnomAD database, including 11,716 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 0.36 (11716 hom., cov: 33)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.937-318T>G		intron_variant	Intron 11 of 11	ENST00000336930.11	NP_001009909.2
LUZP2	NM_001252010.2	c.811-318T>G		intron_variant	Intron 9 of 9		NP_001238939.1
LUZP2	NM_001252008.2	c.679-318T>G		intron_variant	Intron 11 of 11		NP_001238937.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.937-318T>G		intron_variant	Intron 11 of 11	1	NM_001009909.4	ENSP00000336817.6
LUZP2	ENST00000533227.5	c.679-318T>G		intron_variant	Intron 11 of 11	1		ENSP00000432952.1
LUZP2	ENST00000620308.1	c.679-318T>G		intron_variant	Intron 10 of 10	5		ENSP00000480441.1

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54347 AN: 152000 Hom.: 11708 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.357 AC: 54368 AN: 152118 Hom.: 11716 Cov.: 33 AF XY: 0.367 AC XY: 27295 AN XY: 74340

African (AFR) AF: 0.125 AC: 5201 AN: 41548

American (AMR) AF: 0.429 AC: 6553 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3466

East Asian (EAS) AF: 0.788 AC: 4073 AN: 5170

South Asian (SAS) AF: 0.473 AC: 2282 AN: 4820

European-Finnish (FIN) AF: 0.494 AC: 5215 AN: 10566

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28128 AN: 67968

Other (OTH) AF: 0.383 AC: 808 AN: 2112

Alfa AF: 0.366 Hom.: 1487

Bravo AF: 0.343

Asia WGS AF: 0.574 AC: 1996 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.76
PhyloP100		-0.80
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: rs10500993; hg19: chr11-25099782;