NM_001009909.4:c.62+24624C>T

Variant names:

• chr11-24521929-C-T
• rs10500981
• NM_001009909.4:c.62+24624C>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.62+24624C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 151,972 control chromosomes in the GnomAD database, including 607 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 0.084 (607 hom., cov: 32)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.116 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.62+24624C>T		intron	N/A	NP_001009909.2
	LUZP2	NM_001252010.2		c.62+24624C>T		intron	N/A	NP_001238939.1
	LUZP2	NM_001252008.2		c.-193+24624C>T		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.62+24624C>T		intron	N/A	ENSP00000336817.6
	LUZP2	ENST00000533227.5	TSL:1	c.-193+24624C>T		intron	N/A	ENSP00000432952.1
	LUZP2	ENST00000405855.6	TSL:1	n.167+24624C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12769 AN: 151854 Hom.: 607 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.0751

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.0827

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

GnomAD4 genome AF: 0.0840 AC: 12772 AN: 151972 Hom.: 607 Cov.: 32 AF XY: 0.0842 AC XY: 6258 AN XY: 74298

African (AFR) AF: 0.119 AC: 4939 AN: 41446

American (AMR) AF: 0.0970 AC: 1481 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3472

East Asian (EAS) AF: 0.0753 AC: 390 AN: 5178

South Asian (SAS) AF: 0.0434 AC: 209 AN: 4820

European-Finnish (FIN) AF: 0.0926 AC: 973 AN: 10510

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4439 AN: 67960

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

Alfa AF: 0.0725 Hom.: 1062

Bravo AF: 0.0875

Asia WGS AF: 0.0510 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.3
DANN	Benign	0.75
PhyloP100		0.022
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: rs10500981; hg19: chr11-24543475;