3-188865839-C-T

Variant names:

• chr3-188865839-C-T
• rs1983273
• NM_001375462.1:c.1411-361C>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.1411-361C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 151,978 control chromosomes in the GnomAD database, including 5,596 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 0.23 (5596 hom., cov: 32)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 2 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPP	NM_001375462.1	c.1411-361C>T		intron_variant	Intron 9 of 11	ENST00000617246.5	NP_001362391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPP	ENST00000617246.5	c.1411-361C>T		intron_variant	Intron 9 of 11	1	NM_001375462.1	ENSP00000478901.1

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34988 AN: 151860 Hom.: 5588 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.230 AC: 35013 AN: 151978 Hom.: 5596 Cov.: 32 AF XY: 0.244 AC XY: 18135 AN XY: 74266

African (AFR) AF: 0.189 AC: 7812 AN: 41438

American (AMR) AF: 0.408 AC: 6233 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 671 AN: 3468

East Asian (EAS) AF: 0.802 AC: 4136 AN: 5158

South Asian (SAS) AF: 0.400 AC: 1926 AN: 4810

European-Finnish (FIN) AF: 0.245 AC: 2581 AN: 10550

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.162 AC: 11024 AN: 67970

Other (OTH) AF: 0.226 AC: 476 AN: 2106

Alfa AF: 0.179 Hom.: 591

Bravo AF: 0.241

Asia WGS AF: 0.539 AC: 1867 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.38
PhyloP100		-0.50
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: rs1983273; hg19: chr3-188583627;