dbSNP rs374895916: LPP:c.-9-216_-9-214delTCT (chr3-188405894-TTTC-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.-9-216_-9-214delTCT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.81 ( 51358 hom., cov: 0)

Consequence

LPP
NM_001375462.1 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.195

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 3-188405894-TTTC-T is Benign according to our data. Variant chr3-188405894-TTTC-T is described in ClinVar as Benign. ClinVar VariationId is 1242675.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LPP	NM_001375462.1	MANE Select	c.-9-216_-9-214delTCT	intron	N/A	NP_001362391.1	Q93052
LPP	NM_001167671.3		c.-9-216_-9-214delTCT	intron	N/A	NP_001161143.1	Q93052
LPP	NM_001375455.1		c.-9-216_-9-214delTCT	intron	N/A	NP_001362384.1	Q93052

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LPP	ENST00000617246.5	TSL:1 MANE Select	c.-9-217_-9-215delTTC	intron	N/A	ENSP00000478901.1	Q93052
LPP	ENST00000618621.5	TSL:1	c.-9-217_-9-215delTTC	intron	N/A	ENSP00000482617.2	Q93052
LPP	ENST00000414139.6	TSL:4	c.-9-217_-9-215delTTC	intron	N/A	ENSP00000392667.2	Q93052

Frequencies

GnomAD3 genomes

AF:

0.806

AC:

122228

AN:

151588

Hom.:

51334

Cov.:

show subpopulations

Gnomad AFR

AF:

0.550

Gnomad AMI

AF:

0.996

Gnomad AMR

AF:

0.893

Gnomad ASJ

AF:

0.905

Gnomad EAS

AF:

0.757

Gnomad SAS

AF:

0.855

Gnomad FIN

AF:

0.878

Gnomad MID

AF:

0.907

Gnomad NFE

AF:

0.923

Gnomad OTH

AF:

0.848

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

GnomAD4 genome

AF:

0.806

AC:

122296

AN:

151710

Hom.:

51358

Cov.:

AF XY:

0.807

AC XY:

59803

AN XY:

74118

show subpopulations

African (AFR)

AF:

0.549

AC:

22717

AN:

41354

American (AMR)

AF:

0.893

AC:

13620

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.905

AC:

3129

AN:

3458

East Asian (EAS)

AF:

0.758

AC:

3891

AN:

5136

South Asian (SAS)

AF:

0.855

AC:

4120

AN:

4818

European-Finnish (FIN)

AF:

0.878

AC:

9258

AN:

10542

Middle Eastern (MID)

AF:

0.908

AC:

265

AN:

292

European-Non Finnish (NFE)

AF:

0.923

AC:

62598

AN:

67834

Other (OTH)

AF:

0.849

AC:

1790

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

992

1983

2975

3966

4958

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

854

1708

2562

3416

4270

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.894

Hom.:

1785

Asia WGS

AF:

0.766

AC:

2663

AN:

3476

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.20

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over