3-188405910-C-T

Variant names:

• chr3-188405910-C-T
• rs7640006
• NM_001375462.1:c.-9-202C>T

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001375462.1(LPP):​c.-9-202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 151,756 control chromosomes in the GnomAD database, including 51,429 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.81 (51429 hom., cov: 30)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.36
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 3-188405910-C-T is Benign according to our data. Variant chr3-188405910-C-T is described in ClinVar as [Benign]. Clinvar id is 1182384.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 rank	MANE	Protein	UniProt
LPP	NM_001375462.1	c.-9-202C>T		intron_variant	Intron 3 of 11	ENST00000617246.5	NP_001362391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPP	ENST00000617246.5	c.-9-202C>T		intron_variant	Intron 3 of 11	1	NM_001375462.1	ENSP00000478901.1

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122351 AN: 151636 Hom.: 51404 Cov.: 30

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.906

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: 0.807 AC: 122420 AN: 151756 Hom.: 51429 Cov.: 30 AF XY: 0.807 AC XY: 59868 AN XY: 74144

African (AFR) AF: 0.550 AC: 22746 AN: 41340

American (AMR) AF: 0.893 AC: 13622 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3131 AN: 3460

East Asian (EAS) AF: 0.759 AC: 3905 AN: 5148

South Asian (SAS) AF: 0.860 AC: 4144 AN: 4818

European-Finnish (FIN) AF: 0.879 AC: 9269 AN: 10550

Middle Eastern (MID) AF: 0.907 AC: 263 AN: 290

European-Non Finnish (NFE) AF: 0.923 AC: 62642 AN: 67872

Other (OTH) AF: 0.849 AC: 1790 AN: 2108

Alfa AF: 0.839 Hom.: 7139

Bravo AF: 0.795

Asia WGS AF: 0.768 AC: 2671 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.32
PhyloP100		-2.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7640006; hg19: chr3-188123698;