3-188402113-G-A

Position:

• chr3-188402113-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375462.1(LPP):​c.-9-3999G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 151,904 control chromosomes in the GnomAD database, including 29,146 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 0.61 (29146 hom., cov: 31)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

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

Verdict is Benign. Variant got -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 = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPP	NM_001375462.1	c.-9-3999G>A		intron_variant		ENST00000617246.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPP	ENST00000617246.5	c.-9-3999G>A		intron_variant		1	NM_001375462.1	P1

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92154 AN: 151786 Hom.: 29106 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.607 AC: 92257 AN: 151904 Hom.: 29146 Cov.: 31 AF XY: 0.609 AC XY: 45203 AN XY: 74194

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.581

Alfa AF: 0.545 Hom.: 4691

Bravo AF: 0.612

Asia WGS AF: 0.652 AC: 2260 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.085
DANN	Benign	0.36

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030519; hg19: chr3-188119901;