NM_001009909.4:c.63-67598T>C

Variant names:

• chr11-24661571-T-C
• rs4465366
• NM_001009909.4:c.63-67598T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001009909.4(LUZP2):​c.63-67598T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,018 control chromosomes in the GnomAD database, including 24,650 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 0.56 (24650 hom., cov: 32)
• Consequence: LUZP2 NM_001009909.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.63-67598T>C		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.63-67598T>C		intron_variant	Intron 1 of 11	1	NM_001009909.4	ENSP00000336817.6

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85548 AN: 151900 Hom.: 24609 Cov.: 32

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.563 AC: 85642 AN: 152018 Hom.: 24650 Cov.: 32 AF XY: 0.559 AC XY: 41487 AN XY: 74282

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.536

Alfa AF: 0.539 Hom.: 45524

Bravo AF: 0.584

Asia WGS AF: 0.515 AC: 1794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.6
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs4465366; hg19: chr11-24683117;