rs10500995

Positions:

• chr11-25079964-A-G

Variant summary

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

The NM_001009909.4(LUZP2):​c.*1306A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0343 in 152,244 control chromosomes in the GnomAD database, including 216 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 0.034 (216 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LUZP2 NM_001009909.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LUZP2	NM_001009909.4	c.*1306A>G		3_prime_UTR_variant	12/12	ENST00000336930.11	NP_001009909.2
LUZP2	NM_001252008.2	c.*1306A>G		3_prime_UTR_variant	12/12		NP_001238937.1
LUZP2	NM_001252010.2	c.*1306A>G		3_prime_UTR_variant	10/10		NP_001238939.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LUZP2	ENST00000336930.11	c.*1306A>G		3_prime_UTR_variant	12/12	1	NM_001009909.4	ENSP00000336817	P1
LUZP2	ENST00000533227.5	c.*1306A>G		3_prime_UTR_variant	12/12	1		ENSP00000432952
LUZP2	ENST00000620308.1	c.*1306A>G		3_prime_UTR_variant	11/11	5		ENSP00000480441

Frequencies

GnomAD3 genomes AF: 0.0343 AC: 5211 AN: 152126 Hom.: 219 Cov.: 32

Gnomad AFR AF: 0.0976

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.0899

Gnomad SAS AF: 0.00517

Gnomad FIN AF: 0.000659

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00472

Gnomad OTH AF: 0.0310

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 ASJ exome AF: 0.00

GnomAD4 genome AF: 0.0343 AC: 5227 AN: 152244 Hom.: 216 Cov.: 32 AF XY: 0.0331 AC XY: 2467 AN XY: 74456

Gnomad4 AFR AF: 0.0977

Gnomad4 AMR AF: 0.0171

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.0899

Gnomad4 SAS AF: 0.00476

Gnomad4 FIN AF: 0.000659

Gnomad4 NFE AF: 0.00473

Gnomad4 OTH AF: 0.0321

Alfa AF: 0.0114 Hom.: 46

Bravo AF: 0.0384

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.49

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: rs10500995; hg19: chr11-25101510;