Variant 3-188524893-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001375462.1(LPP):c.429+106G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 215,504 control chromosomes in the GnomAD database, including 52,155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 598 hom., cov: 0)

Exomes 𝑓: 0.68 ( 51557 hom. )

Consequence

LPP
NM_001375462.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.35

Variant links:

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]

LPP links:

LPP (HGNC:):

LPP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BP6

Variant 3-188524893-G-T is Benign according to our data. Variant chr3-188524893-G-T is described in ClinVar as [Benign]. Clinvar id is 1246296.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPP	NM_001375462.1 linkuse as main transcript	c.429+106G>T		intron_variant		ENST00000617246.5	NP_001362391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPP	ENST00000617246.5 linkuse as main transcript	c.429+106G>T		intron_variant		1	NM_001375462.1	ENSP00000478901.1		Q93052

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

6884

AN:

17412

Hom.:

596

Cov.:

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.0263

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.260

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0512

Gnomad MID

AF:

0.182

Gnomad NFE

AF:

0.0855

Gnomad OTH

AF:

0.332

GnomAD4 exome

AF:

0.684

AC:

135467

AN:

198064

Hom.:

51557

AF XY:

0.676

AC XY:

64152

AN XY:

94964

show subpopulations

Gnomad4 AFR exome

AF:

0.481

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.536

Gnomad4 EAS exome

AF:

0.783

Gnomad4 SAS exome

AF:

0.494

Gnomad4 FIN exome

AF:

0.313

Gnomad4 NFE exome

AF:

0.716

Gnomad4 OTH exome

AF:

0.635

GnomAD4 genome

AF:

0.396

AC:

6900

AN:

17440

Hom.:

598

Cov.:

AF XY:

0.394

AC XY:

3301

AN XY:

8368

show subpopulations

Gnomad4 AFR

AF:

0.467

Gnomad4 AMR

AF:

0.289

Gnomad4 ASJ

AF:

0.321

Gnomad4 EAS

AF:

0.260

Gnomad4 SAS

AF:

0.106

Gnomad4 FIN

AF:

0.0512

Gnomad4 NFE

AF:

0.0851

Gnomad4 OTH

AF:

0.332

Alfa

AF:

0.300

Hom.:

212

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.77

DANN

Benign

0.30

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over