rs373734498

Variant names:

• chr3-188524905-T-A
• rs373734498
• NM_001375462.1:c.429+118T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-188524905-T-A
• chr3-188524905-T-C
• chr3-188524905-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001375462.1(LPP):​c.429+118T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0000094 (0 hom., cov: 19)
  • Exomes 𝑓: 0.00014 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.342
• 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPP	NM_001375462.1	c.429+118T>A		intron_variant	Intron 6 of 11	ENST00000617246.5	NP_001362391.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPP	ENST00000617246.5	c.429+118T>A		intron_variant	Intron 6 of 11	1	NM_001375462.1	ENSP00000478901.1

Frequencies

GnomAD3 genomes AF: 0.00000943 AC: 1 AN: 106066 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000206

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000142 AC: 20 AN: 141148 Hom.: 0 AF XY: 0.0000962 AC XY: 7 AN XY: 72792

African (AFR) AF: 0.00 AC: 0 AN: 4816

American (AMR) AF: 0.00 AC: 0 AN: 4814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4604

East Asian (EAS) AF: 0.00 AC: 0 AN: 21320

South Asian (SAS) AF: 0.00 AC: 0 AN: 8378

European-Finnish (FIN) AF: 0.000108 AC: 1 AN: 9240

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 582

European-Non Finnish (NFE) AF: 0.000214 AC: 17 AN: 79390

Other (OTH) AF: 0.000250 AC: 2 AN: 8004

GnomAD4 genome AF: 0.00000943 AC: 1 AN: 106066 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 50844

African (AFR) AF: 0.00 AC: 0 AN: 29106

American (AMR) AF: 0.00 AC: 0 AN: 10078

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2578

East Asian (EAS) AF: 0.00 AC: 0 AN: 4306

South Asian (SAS) AF: 0.00 AC: 0 AN: 3056

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6154

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 212

European-Non Finnish (NFE) AF: 0.0000206 AC: 1 AN: 48614

Other (OTH) AF: 0.00 AC: 0 AN: 1444

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		-0.34

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: rs373734498; hg19: chr3-188242693;