Variant chr3-188406031-T-G 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.-9-81T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 1,247,090 control chromosomes in the GnomAD database, including 505,305 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.81 ( 51998 hom., cov: 32)

Exomes 𝑓: 0.91 ( 453307 hom. )

Consequence

LPP
NM_001375462.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.847

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:

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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=-0.85).

BP6

Variant 3-188406031-T-G is Benign according to our data. Variant chr3-188406031-T-G is described in ClinVar as [Benign]. Clinvar id is 1266998.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 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.-9-81T>G		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.-9-81T>G		intron_variant		1	NM_001375462.1	ENSP00000478901	P1

Frequencies

GnomAD3 genomes

AF:

0.810

AC:

123143

AN:

152012

Hom.:

51975

Cov.:

show subpopulations

Gnomad AFR

AF:

0.551

Gnomad AMI

AF:

0.997

Gnomad AMR

AF:

0.900

Gnomad ASJ

AF:

0.906

Gnomad EAS

AF:

0.758

Gnomad SAS

AF:

0.863

Gnomad FIN

AF:

0.880

Gnomad MID

AF:

0.908

Gnomad NFE

AF:

0.927

Gnomad OTH

AF:

0.849

GnomAD4 exome

AF:

0.907

AC:

993483

AN:

1094960

Hom.:

453307

AF XY:

0.907

AC XY:

497511

AN XY:

548496

show subpopulations

Gnomad4 AFR exome

AF:

0.546

Gnomad4 AMR exome

AF:

0.924

Gnomad4 ASJ exome

AF:

0.909

Gnomad4 EAS exome

AF:

0.786

Gnomad4 SAS exome

AF:

0.864

Gnomad4 FIN exome

AF:

0.887

Gnomad4 NFE exome

AF:

0.929

Gnomad4 OTH exome

AF:

0.887

GnomAD4 genome

AF:

0.810

AC:

123209

AN:

152130

Hom.:

51998

Cov.:

AF XY:

0.811

AC XY:

60294

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.551

Gnomad4 AMR

AF:

0.900

Gnomad4 ASJ

AF:

0.906

Gnomad4 EAS

AF:

0.759

Gnomad4 SAS

AF:

0.864

Gnomad4 FIN

AF:

0.880

Gnomad4 NFE

AF:

0.927

Gnomad4 OTH

AF:

0.851

Alfa

AF:

0.848

Hom.:

13578

Bravo

AF:

0.798

Asia WGS

AF:

0.770

AC:

2677

AN:

3478

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	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.3

DANN

Benign

0.34

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