Genetic Variant NM_001375462.1:c.429+106_429+117delGTCCGTCCTTCC (chr3-188524885-TTCCTTCCGTCCG-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001375462.1(LPP):c.429+106_429+117delGTCCGTCCTTCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 250,740 control chromosomes in the GnomAD database, including 10,311 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.52 ( 5588 hom., cov: 0)

Exomes 𝑓: 0.33 ( 10311 hom. )

Failed GnomAD Quality Control

Consequence

LPP
NM_001375462.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.678

Publications

0 publications found

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 was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 3-188524885-TTCCTTCCGTCCG-T is Benign according to our data. Variant chr3-188524885-TTCCTTCCGTCCG-T is described in ClinVar as [Benign]. Clinvar id is 1260569.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPP	NM_001375462.1 link	c.429+106_429+117delGTCCGTCCTTCC		intron_variant	Intron 6 of 11	ENST00000617246.5	NP_001362391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPP	ENST00000617246.5 link	c.429+99_429+110delTCCTTCCGTCCG		intron_variant	Intron 6 of 11	1	NM_001375462.1	ENSP00000478901.1		Q93052

Frequencies

GnomAD3 genomes

AF:

0.520

AC:

36947

AN:

71104

Hom.:

5585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.407

Gnomad AMI

AF:

0.515

Gnomad AMR

AF:

0.536

Gnomad ASJ

AF:

0.527

Gnomad EAS

AF:

0.474

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.530

Gnomad MID

AF:

0.571

Gnomad NFE

AF:

0.568

Gnomad OTH

AF:

0.532

GnomAD4 exome

AF:

0.328

AC:

82334

AN:

250740

Hom.:

10311

AF XY:

0.337

AC XY:

43540

AN XY:

129082

show subpopulations

African (AFR)

AF:

0.185

AC:

1480

AN:

8016

American (AMR)

AF:

0.282

AC:

2093

AN:

7416

Ashkenazi Jewish (ASJ)

AF:

0.404

AC:

2531

AN:

6270

East Asian (EAS)

AF:

0.411

AC:

967

AN:

2352

South Asian (SAS)

AF:

0.353

AC:

5468

AN:

15478

European-Finnish (FIN)

AF:

0.443

AC:

8202

AN:

18528

Middle Eastern (MID)

AF:

0.361

AC:

543

AN:

1504

European-Non Finnish (NFE)

AF:

0.315

AC:

56158

AN:

178258

Other (OTH)

AF:

0.379

AC:

4892

AN:

12918

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

2313

4626

6938

9251

11564

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.519

AC:

36966

AN:

71164

Hom.:

5588

Cov.:

AF XY:

0.516

AC XY:

17245

AN XY:

33422

show subpopulations

African (AFR)

AF:

0.407

AC:

7195

AN:

17694

American (AMR)

AF:

0.536

AC:

3551

AN:

6626

Ashkenazi Jewish (ASJ)

AF:

0.527

AC:

931

AN:

1768

East Asian (EAS)

AF:

0.474

AC:

147

AN:

310

South Asian (SAS)

AF:

0.536

AC:

1095

AN:

2044

European-Finnish (FIN)

AF:

0.530

AC:

2123

AN:

4004

Middle Eastern (MID)

AF:

0.564

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.568

AC:

20975

AN:

36928

Other (OTH)

AF:

0.533

AC:

551

AN:

1034

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

975

1949

2924

3898

4873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.236

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jun 19, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.68

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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NM_001375462.1:c.429+106_429+117delGTCCGTCCTTCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over