Variant 3-188524913-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.429+126T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 139,178 control chromosomes in the GnomAD database, including 33,517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 33517 hom., cov: 21)

Exomes 𝑓: 0.79 ( 140508 hom. )

Failed GnomAD Quality Control

Consequence

LPP
NM_001375462.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.20

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=-0.97).

BP6

Variant 3-188524913-T-G is Benign according to our data. Variant chr3-188524913-T-G is described in ClinVar as [Benign]. Clinvar id is 1182900.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPP	NM_001375462.1 link	c.429+126T>G		intron_variant		ENST00000617246.5	NP_001362391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPP	ENST00000617246.5 link	c.429+126T>G		intron_variant		1	NM_001375462.1	ENSP00000478901.1		Q93052

Frequencies

GnomAD3 genomes

AF:

0.676

AC:

94089

AN:

139110

Hom.:

33516

Cov.:

show subpopulations

Gnomad AFR

AF:

0.444

Gnomad AMI

AF:

0.615

Gnomad AMR

AF:

0.735

Gnomad ASJ

AF:

0.657

Gnomad EAS

AF:

0.888

Gnomad SAS

AF:

0.696

Gnomad FIN

AF:

0.688

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.780

Gnomad OTH

AF:

0.693

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.786

AC:

349556

AN:

444612

Hom.:

140508

AF XY:

0.780

AC XY:

178634

AN XY:

228916

show subpopulations

Gnomad4 AFR exome

AF:

0.464

Gnomad4 AMR exome

AF:

0.719

Gnomad4 ASJ exome

AF:

0.668

Gnomad4 EAS exome

AF:

0.867

Gnomad4 SAS exome

AF:

0.688

Gnomad4 FIN exome

AF:

0.727

Gnomad4 NFE exome

AF:

0.813

Gnomad4 OTH exome

AF:

0.752

GnomAD4 genome

AF:

0.676

AC:

94105

AN:

139178

Hom.:

33517

Cov.:

AF XY:

0.670

AC XY:

44694

AN XY:

66658

show subpopulations

Gnomad4 AFR

AF:

0.444

Gnomad4 AMR

AF:

0.735

Gnomad4 ASJ

AF:

0.657

Gnomad4 EAS

AF:

0.888

Gnomad4 SAS

AF:

0.696

Gnomad4 FIN

AF:

0.688

Gnomad4 NFE

AF:

0.780

Gnomad4 OTH

AF:

0.696

Alfa

AF:

0.564

Hom.:

1292

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.4

DANN

Benign

0.33

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