3-188524885-TTCCTTCCGTCCG-T

Position:

• chr3-188524885-TTCCTTCCGTCCG-T

Variant summary

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

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. 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.678

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 3-188524885-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/exons	MANE	Protein	UniProt
LPP	NM_001375462.1	c.429+106_429+117delGTCCGTCCTTCC		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+106_429+117delGTCCGTCCTTCC		intron_variant		1	NM_001375462.1	ENSP00000478901.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 36947 AN: 71104 Hom.: 5585 Cov.: 0 FAILED QC

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

Gnomad4 AFR exome AF: 0.185

Gnomad4 AMR exome AF: 0.282

Gnomad4 ASJ exome AF: 0.404

Gnomad4 EAS exome AF: 0.411

Gnomad4 SAS exome AF: 0.353

Gnomad4 FIN exome AF: 0.443

Gnomad4 NFE exome AF: 0.315

Gnomad4 OTH exome AF: 0.379

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.519 AC: 36966 AN: 71164 Hom.: 5588 Cov.: 0 AF XY: 0.516 AC XY: 17245 AN XY: 33422

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.527

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.536

Gnomad4 FIN AF: 0.530

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.533

Alfa AF: 0.236 Hom.: 0

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 19, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs542563933; hg19: chr3-188242673;