chr3-188405894-TTTC-T

Position:

• chr3-188405894-TTTC-T

Variant summary

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

The NM_001375462.1(LPP):​c.-9-216_-9-214del 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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.195

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 3-188405894-TTTC-T is Benign according to our data. Variant chr3-188405894-TTTC-T is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPP	NM_001375462.1	c.-9-216_-9-214del		intron_variant		ENST00000617246.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPP	ENST00000617246.5	c.-9-216_-9-214del		intron_variant		1	NM_001375462.1	P1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122228 AN: 151588 Hom.: 51334 Cov.: 0

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.: 0 AF XY: 0.807 AC XY: 59803 AN XY: 74118

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.849

Alfa AF: 0.894 Hom.: 1785

Asia WGS AF: 0.766 AC: 2663 AN: 3476

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

- -

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: rs374895916; hg19: chr3-188123682;