3-188524881-TTCCTTCCTTCCGTCCG-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+121del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 634,180 control chromosomes in the GnomAD database, including 94,438 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.55 (12423 hom., cov: 0)
  • Exomes 𝑓: 0.47 (82015 hom.)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.862

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-188524881-TTCCTTCCTTCCGTCCG-T is Benign according to our data. Variant chr3-188524881-TTCCTTCCTTCCGTCCG-T is described in ClinVar as [Benign]. Clinvar id is 1234700.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPP	NM_001375462.1	c.429+106_429+121del		intron_variant		ENST00000617246.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPP	ENST00000617246.5	c.429+106_429+121del		intron_variant		1	NM_001375462.1	P1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 54647 AN: 99238 Hom.: 12433 Cov.: 0

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.534

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.549

GnomAD4 exome AF: 0.467 AC: 249732 AN: 534910 Hom.: 82015 AF XY: 0.462 AC XY: 126291 AN XY: 273478

Gnomad4 AFR exome AF: 0.193

Gnomad4 AMR exome AF: 0.438

Gnomad4 ASJ exome AF: 0.399

Gnomad4 EAS exome AF: 0.832

Gnomad4 SAS exome AF: 0.357

Gnomad4 FIN exome AF: 0.385

Gnomad4 NFE exome AF: 0.472

Gnomad4 OTH exome AF: 0.450

GnomAD4 genome AF: 0.550 AC: 54642 AN: 99270 Hom.: 12423 Cov.: 0 AF XY: 0.553 AC XY: 26216 AN XY: 47412

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.549

Alfa AF: 0.284 Hom.: 2

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: rs200398269; hg19: chr3-188242669;