rs9820681

Variant names:

• chr3-188398996-G-A
• rs9820681
• NM_001375462.1:c.-9-7116G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-188398996-G-A
• chr3-188398996-G-C
• chr3-188398996-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001375462.1(LPP):​c.-9-7116G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,200 control chromosomes in the GnomAD database, including 47,141 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 0.76 (47141 hom., cov: 33)
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 5 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPP	NM_001375462.1	c.-9-7116G>A		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.-9-7116G>A		intron_variant	Intron 3 of 11	1	NM_001375462.1	ENSP00000478901.1

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115506 AN: 152082 Hom.: 47120 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.910

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.814

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.759 AC: 115566 AN: 152200 Hom.: 47141 Cov.: 33 AF XY: 0.764 AC XY: 56863 AN XY: 74418

African (AFR) AF: 0.428 AC: 17762 AN: 41460

American (AMR) AF: 0.876 AC: 13393 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3170 AN: 3470

East Asian (EAS) AF: 0.793 AC: 4110 AN: 5182

South Asian (SAS) AF: 0.892 AC: 4306 AN: 4828

European-Finnish (FIN) AF: 0.878 AC: 9319 AN: 10616

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60677 AN: 68030

Other (OTH) AF: 0.816 AC: 1727 AN: 2116

Alfa AF: 0.852 Hom.: 83927

Bravo AF: 0.741

Asia WGS AF: 0.787 AC: 2737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		0.54
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs9820681; hg19: chr3-188116784;