NM_001009909.4:c.396+7880T>C

Variant names:

• chr11-24771188-T-C
• rs2631407
• NM_001009909.4:c.396+7880T>C

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+7880T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 150,686 control chromosomes in the GnomAD database, including 33,917 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 (33917 hom., cov: 28)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001009909.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUZP2	NM_001009909.4	MANE Select	c.396+7880T>C		intron	N/A	NP_001009909.2
	LUZP2	NM_001252010.2		c.396+7880T>C		intron	N/A	NP_001238939.1
	LUZP2	NM_001252008.2		c.138+7880T>C		intron	N/A	NP_001238937.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUZP2	ENST00000336930.11	TSL:1 MANE Select	c.396+7880T>C		intron	N/A	ENSP00000336817.6
	LUZP2	ENST00000533227.5	TSL:1	c.138+7880T>C		intron	N/A	ENSP00000432952.1
	LUZP2	ENST00000405855.6	TSL:1	n.501+7880T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.669 AC: 100725 AN: 150566 Hom.: 33880 Cov.: 28

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.669 AC: 100814 AN: 150686 Hom.: 33917 Cov.: 28 AF XY: 0.662 AC XY: 48677 AN XY: 73544

African (AFR) AF: 0.708 AC: 29124 AN: 41138

American (AMR) AF: 0.583 AC: 8792 AN: 15082

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2281 AN: 3456

East Asian (EAS) AF: 0.454 AC: 2292 AN: 5048

South Asian (SAS) AF: 0.624 AC: 2965 AN: 4752

European-Finnish (FIN) AF: 0.646 AC: 6666 AN: 10320

Middle Eastern (MID) AF: 0.606 AC: 172 AN: 284

European-Non Finnish (NFE) AF: 0.690 AC: 46690 AN: 67634

Other (OTH) AF: 0.653 AC: 1357 AN: 2078

Alfa AF: 0.600 Hom.: 1982

Bravo AF: 0.667

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		-0.018
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: rs2631407; hg19: chr11-24792734;