11-24715070-T-A

Variant names:

• chr11-24715070-T-A
• rs2631439
• NM_001009909.4:c.63-14099T>A

Variant summary

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

The NM_001009909.4(LUZP2):​c.63-14099T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,070 control chromosomes in the GnomAD database, including 4,280 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 0.19 (4280 hom., cov: 32)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.63-14099T>A		intron_variant	Intron 1 of 11	ENST00000336930.11	NP_001009909.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.63-14099T>A		intron_variant	Intron 1 of 11	1	NM_001009909.4	ENSP00000336817.6

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29137 AN: 151952 Hom.: 4262 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0919

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.192 AC: 29199 AN: 152070 Hom.: 4280 Cov.: 32 AF XY: 0.194 AC XY: 14392 AN XY: 74346

African (AFR) AF: 0.388 AC: 16058 AN: 41416

American (AMR) AF: 0.237 AC: 3622 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.147 AC: 759 AN: 5160

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4818

European-Finnish (FIN) AF: 0.0601 AC: 638 AN: 10612

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0919 AC: 6253 AN: 68006

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.0403 Hom.: 40

Bravo AF: 0.213

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.6
DANN	Benign	0.83
PhyloP100		0.31
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: rs2631439; hg19: chr11-24736616;