NM_001009909.4:c.*1306A>G

Variant names:

• chr11-25079964-A-G
• rs10500995
• NM_001009909.4:c.*1306A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0952 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.*1306A>G		3_prime_UTR	Exon 12 of 12	NP_001009909.2
	LUZP2	NM_001252010.2		c.*1306A>G		3_prime_UTR	Exon 10 of 10	NP_001238939.1
	LUZP2	NM_001252008.2		c.*1306A>G		3_prime_UTR	Exon 12 of 12	NP_001238937.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LUZP2	ENST00000336930.11	TSL:1 MANE Select	c.*1306A>G		3_prime_UTR	Exon 12 of 12	ENSP00000336817.6
	LUZP2	ENST00000533227.5	TSL:1	c.*1306A>G		3_prime_UTR	Exon 12 of 12	ENSP00000432952.1
	LUZP2	ENST00000620308.1	TSL:5	c.*1306A>G		3_prime_UTR	Exon 11 of 11	ENSP00000480441.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0977 AC: 4055 AN: 41518

American (AMR) AF: 0.0171 AC: 262 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00317 AC: 11 AN: 3466

East Asian (EAS) AF: 0.0899 AC: 466 AN: 5182

South Asian (SAS) AF: 0.00476 AC: 23 AN: 4828

European-Finnish (FIN) AF: 0.000659 AC: 7 AN: 10626

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00473 AC: 322 AN: 68012

Other (OTH) AF: 0.0321 AC: 68 AN: 2116

Alfa AF: 0.0150 Hom.: 89

Bravo AF: 0.0384

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.49
PhyloP100		-0.51
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: rs10500995; hg19: chr11-25101510;