NM_001318100.2:c.*192C>A

Variant names:

• chr10-101007360-C-A
• rs701836
• NM_001318100.2:c.*192C>A

Variant summary

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

The NM_001318100.2(LZTS2):​c.*192C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 1,412,228 control chromosomes in the GnomAD database, including 50,233 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 0.29 (6891 hom., cov: 33)
  • Exomes 𝑓: 0.25 (43342 hom.)
• Consequence: LZTS2 NM_001318100.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 19 publications found

Genes affected

LZTS2 (HGNC:29381): (leucine zipper tumor suppressor 2) The protein encoded by this gene belongs to the leucine zipper tumor suppressor family of proteins, which function in transcription regulation and cell cycle control. This family member can repress beta-catenin-mediated transcriptional activation and is a negative regulator of the Wnt signaling pathway. It negatively regulates microtubule severing at centrosomes, and is necessary for central spindle formation and cytokinesis completion. It is implicated in cancer, where it may inhibit cell proliferation and decrease susceptibility to tumor development. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318100.2. 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
	LZTS2	NM_001318100.2	MANE Select	c.*192C>A		3_prime_UTR	Exon 5 of 5	NP_001305029.1
	LZTS2	NM_001318099.2		c.*192C>A		3_prime_UTR	Exon 5 of 5	NP_001305028.1
	LZTS2	NM_001394950.1		c.*192C>A		3_prime_UTR	Exon 5 of 5	NP_001381879.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LZTS2	ENST00000454422.2	TSL:2 MANE Select	c.*192C>A		3_prime_UTR	Exon 5 of 5	ENSP00000416972.2
	LZTS2	ENST00000370220.1	TSL:1	c.*192C>A		3_prime_UTR	Exon 4 of 4	ENSP00000359240.1
	LZTS2	ENST00000370223.7	TSL:1	c.*192C>A		3_prime_UTR	Exon 5 of 5	ENSP00000359243.3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43819 AN: 152026 Hom.: 6877 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.254 AC: 320452 AN: 1260084 Hom.: 43342 Cov.: 31 AF XY: 0.254 AC XY: 154954 AN XY: 609084

African (AFR) AF: 0.385 AC: 10465 AN: 27174

American (AMR) AF: 0.349 AC: 6232 AN: 17846

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 3451 AN: 18478

East Asian (EAS) AF: 0.557 AC: 18118 AN: 32500

South Asian (SAS) AF: 0.290 AC: 17074 AN: 58834

European-Finnish (FIN) AF: 0.208 AC: 6232 AN: 29898

Middle Eastern (MID) AF: 0.226 AC: 974 AN: 4304

European-Non Finnish (NFE) AF: 0.239 AC: 243934 AN: 1018688

Other (OTH) AF: 0.267 AC: 13972 AN: 52362

GnomAD4 genome AF: 0.288 AC: 43860 AN: 152144 Hom.: 6891 Cov.: 33 AF XY: 0.290 AC XY: 21557 AN XY: 74386

African (AFR) AF: 0.366 AC: 15205 AN: 41488

American (AMR) AF: 0.312 AC: 4774 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 683 AN: 3472

East Asian (EAS) AF: 0.547 AC: 2831 AN: 5174

South Asian (SAS) AF: 0.306 AC: 1480 AN: 4830

European-Finnish (FIN) AF: 0.200 AC: 2119 AN: 10604

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15949 AN: 67962

Other (OTH) AF: 0.270 AC: 571 AN: 2114

Alfa AF: 0.254 Hom.: 14352

Bravo AF: 0.304

Asia WGS AF: 0.406 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		0.029
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs701836; hg19: chr10-102767117; COSMIC: COSV64652069; COSMIC: COSV64652069;