NM_001375462.1:c.1114-5158T>C

Variant names:

• chr3-188703109-T-C
• rs1152846
• NM_001375462.1:c.1114-5158T>C

Variant summary

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

The NM_001375462.1(LPP):​c.1114-5158T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,124 control chromosomes in the GnomAD database, including 36,828 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 0.69 (36828 hom., cov: 32)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 13 publications found

Genes affected

LPP (HGNC:6679): (LIM domain containing preferred translocation partner in lipoma) This gene encodes a member of a subfamily of LIM domain proteins that are characterized by an N-terminal proline-rich region and three C-terminal LIM domains. The encoded protein localizes to the cell periphery in focal adhesions and may be involved in cell-cell adhesion and cell motility. This protein also shuttles through the nucleus and may function as a transcriptional co-activator. This gene is located at the junction of certain disease-related chromosomal translocations, which result in the expression of chimeric proteins that may promote tumor growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPP	NM_001375462.1	MANE Select	c.1114-5158T>C		intron	N/A	NP_001362391.1	Q93052
	LPP	NM_001167671.3		c.1114-5158T>C		intron	N/A	NP_001161143.1	Q93052
	LPP	NM_001375455.1		c.1114-5158T>C		intron	N/A	NP_001362384.1	Q93052

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPP	ENST00000617246.5	TSL:1 MANE Select	c.1114-5158T>C		intron	N/A	ENSP00000478901.1	Q93052
	LPP	ENST00000618621.5	TSL:1	c.1114-5158T>C		intron	N/A	ENSP00000482617.2	Q93052
	LPP	ENST00000414139.6	TSL:4	c.1114-5158T>C		intron	N/A	ENSP00000392667.2	Q93052

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104717 AN: 152006 Hom.: 36788 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.697

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

GnomAD4 genome AF: 0.689 AC: 104820 AN: 152124 Hom.: 36828 Cov.: 32 AF XY: 0.681 AC XY: 50617 AN XY: 74356

African (AFR) AF: 0.671 AC: 27822 AN: 41488

American (AMR) AF: 0.621 AC: 9498 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2445 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1455 AN: 5168

South Asian (SAS) AF: 0.585 AC: 2820 AN: 4818

European-Finnish (FIN) AF: 0.662 AC: 7017 AN: 10594

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51420 AN: 67986

Other (OTH) AF: 0.701 AC: 1481 AN: 2112

Alfa AF: 0.728 Hom.: 142908

Bravo AF: 0.683

Asia WGS AF: 0.460 AC: 1605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		-0.13
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: rs1152846; hg19: chr3-188420897;