rs144299808

Variant names:

• chr3-188524917-T-A
• rs144299808
• NM_001375462.1:c.429+130T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-188524917-T-A
• chr3-188524917-T-C
• chr3-188524917-T-G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001375462.1(LPP):​c.429+130T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000627 in 639,788 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00077 (3 hom., cov: 24)
  • Exomes 𝑓: 0.00059 (5 hom.)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 2 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High AC in GnomAd4 at 112 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001375462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPP	NM_001375462.1	MANE Select	c.429+130T>A		intron	N/A	NP_001362391.1	Q93052
	LPP	NM_001167671.3		c.429+130T>A		intron	N/A	NP_001161143.1	Q93052
	LPP	NM_001375455.1		c.429+130T>A		intron	N/A	NP_001362384.1	Q93052

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPP	ENST00000617246.5	TSL:1 MANE Select	c.429+130T>A		intron	N/A	ENSP00000478901.1	Q93052
	LPP	ENST00000618621.5	TSL:1	c.429+130T>A		intron	N/A	ENSP00000482617.2	Q93052
	LPP	ENST00000414139.6	TSL:4	c.429+130T>A		intron	N/A	ENSP00000392667.2	Q93052

Frequencies

GnomAD3 genomes AF: 0.000762 AC: 111 AN: 145714 Hom.: 3 Cov.: 24

Gnomad AFR AF: 0.000708

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00195

Gnomad ASJ AF: 0.000292

Gnomad EAS AF: 0.000200

Gnomad SAS AF: 0.000446

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0162

Gnomad NFE AF: 0.000570

Gnomad OTH AF: 0.00404

GnomAD4 exome AF: 0.000585 AC: 289 AN: 493996 Hom.: 5 AF XY: 0.000641 AC XY: 163 AN XY: 254482

African (AFR) AF: 0.00108 AC: 11 AN: 10162

American (AMR) AF: 0.00139 AC: 20 AN: 14424

Ashkenazi Jewish (ASJ) AF: 0.000168 AC: 2 AN: 11870

East Asian (EAS) AF: 0.00 AC: 0 AN: 27396

South Asian (SAS) AF: 0.000414 AC: 13 AN: 31436

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31682

Middle Eastern (MID) AF: 0.0139 AC: 31 AN: 2224

European-Non Finnish (NFE) AF: 0.000536 AC: 182 AN: 339336

Other (OTH) AF: 0.00118 AC: 30 AN: 25466

GnomAD4 genome AF: 0.000768 AC: 112 AN: 145792 Hom.: 3 Cov.: 24 AF XY: 0.000668 AC XY: 47 AN XY: 70350

African (AFR) AF: 0.000732 AC: 29 AN: 39642

American (AMR) AF: 0.00195 AC: 28 AN: 14388

Ashkenazi Jewish (ASJ) AF: 0.000292 AC: 1 AN: 3428

East Asian (EAS) AF: 0.000201 AC: 1 AN: 4976

South Asian (SAS) AF: 0.000447 AC: 2 AN: 4476

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9032

Middle Eastern (MID) AF: 0.0175 AC: 5 AN: 286

European-Non Finnish (NFE) AF: 0.000570 AC: 38 AN: 66668

Other (OTH) AF: 0.00400 AC: 8 AN: 1998

Alfa AF: 0.00 Hom.: 511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.53
PhyloP100		-0.90
Mutation Taster		=100/0	polymorphism

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: rs144299808; hg19: chr3-188242705;