3-188524971-C-CT

Position:

• chr3-188524971-C-CT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001375462.1(LPP):​c.429+199dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.76 (35631 hom., cov: 0)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.28

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-188524971-C-CT is Benign according to our data. Variant chr3-188524971-C-CT is described in ClinVar as [Benign]. Clinvar id is 1237160.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPP	NM_001375462.1	c.429+199dupT		intron_variant		ENST00000617246.5	NP_001362391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPP	ENST00000617246.5	c.429+199dupT		intron_variant		1	NM_001375462.1	ENSP00000478901.1

Frequencies

GnomAD3 genomes AF: 0.760 AC: 90619 AN: 119264 Hom.: 35647 Cov.: 0

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.927

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.754

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.760 AC: 90585 AN: 119238 Hom.: 35631 Cov.: 0 AF XY: 0.757 AC XY: 41929 AN XY: 55412

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.767

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs540192956; hg19: chr3-188242759;