NM_001009909.4:c.396+64712C>T

Variant names:

• chr11-24828020-C-T
• rs10500991
• NM_001009909.4:c.396+64712C>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+64712C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 117,938 control chromosomes in the GnomAD database, including 1,062 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 0.13 (1062 hom., cov: 31)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 5 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.396+64712C>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+64712C>T		intron_variant	Intron 5 of 11	1	NM_001009909.4	ENSP00000336817.6

Frequencies

GnomAD3 genomes AF: 0.133 AC: 15636 AN: 117818 Hom.: 1060 Cov.: 31

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0764

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.133 AC: 15647 AN: 117938 Hom.: 1062 Cov.: 31 AF XY: 0.132 AC XY: 7472 AN XY: 56450

African (AFR) AF: 0.0338 AC: 1114 AN: 33006

American (AMR) AF: 0.226 AC: 2344 AN: 10360

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 294 AN: 2828

East Asian (EAS) AF: 0.0767 AC: 281 AN: 3664

South Asian (SAS) AF: 0.128 AC: 395 AN: 3086

European-Finnish (FIN) AF: 0.164 AC: 1172 AN: 7166

Middle Eastern (MID) AF: 0.104 AC: 24 AN: 230

European-Non Finnish (NFE) AF: 0.176 AC: 9707 AN: 55302

Other (OTH) AF: 0.126 AC: 194 AN: 1534

Alfa AF: 0.126 Hom.: 3178

Bravo AF: 0.104

Asia WGS AF: 0.0670 AC: 232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.82
PhyloP100		-0.40
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: rs10500991; hg19: chr11-24849566;