rs9860547

Variant names:

• chr3-188411191-G-A
• rs9860547
• NM_001375462.1:c.193+4878G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-188411191-G-A
• chr3-188411191-G-T

Variant summary

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

The NM_001375462.1(LPP):​c.193+4878G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,772 control chromosomes in the GnomAD database, including 10,594 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 0.34 (10594 hom., cov: 32)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 29 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 = 0.451 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.193+4878G>A		intron	N/A	NP_001362391.1	Q93052
	LPP	NM_001167671.3		c.193+4878G>A		intron	N/A	NP_001161143.1	Q93052
	LPP	NM_001375455.1		c.193+4878G>A		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.193+4878G>A		intron	N/A	ENSP00000478901.1	Q93052
	LPP	ENST00000618621.5	TSL:1	c.193+4878G>A		intron	N/A	ENSP00000482617.2	Q93052
	LPP	ENST00000414139.6	TSL:4	c.193+4878G>A		intron	N/A	ENSP00000392667.2	Q93052

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51754 AN: 151654 Hom.: 10602 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.341 AC: 51737 AN: 151772 Hom.: 10594 Cov.: 32 AF XY: 0.339 AC XY: 25102 AN XY: 74154

African (AFR) AF: 0.107 AC: 4416 AN: 41404

American (AMR) AF: 0.407 AC: 6203 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1692 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1701 AN: 5156

South Asian (SAS) AF: 0.308 AC: 1478 AN: 4802

European-Finnish (FIN) AF: 0.365 AC: 3836 AN: 10502

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30914 AN: 67904

Other (OTH) AF: 0.381 AC: 803 AN: 2106

Alfa AF: 0.377 Hom.: 1680

Bravo AF: 0.335

Asia WGS AF: 0.287 AC: 999 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	0.83
DANN	Benign	0.43
PhyloP100		-0.68
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: rs9860547; hg19: chr3-188128979;