NM_001375462.1:c.429+122T>A

Variant names:

• chr3-188524909-T-A
• rs369579197
• NM_001375462.1:c.429+122T>A

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+122T>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 0.00016 (1 hom., cov: 20)
  • Exomes 𝑓: 0.00024 (3 hom.)
  • Failed GnomAD Quality Control
• Consequence: LPP NM_001375462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215
• Publications: 1 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 22 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPP	NM_001375462.1	c.429+122T>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+122T>A		intron_variant	Intron 6 of 11	1	NM_001375462.1	ENSP00000478901.1

Frequencies

GnomAD3 genomes AF: 0.000165 AC: 22 AN: 133674 Hom.: 1 Cov.: 20

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000423

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00157

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000110

Gnomad OTH AF: 0.000549

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000240 AC: 81 AN: 337434 Hom.: 3 AF XY: 0.000231 AC XY: 41 AN XY: 177108

African (AFR) AF: 0.00 AC: 0 AN: 7696

American (AMR) AF: 0.00 AC: 0 AN: 11820

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10114

East Asian (EAS) AF: 0.000478 AC: 12 AN: 25096

South Asian (SAS) AF: 0.000180 AC: 4 AN: 22224

European-Finnish (FIN) AF: 0.00154 AC: 43 AN: 27998

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1714

European-Non Finnish (NFE) AF: 0.0000758 AC: 16 AN: 211084

Other (OTH) AF: 0.000305 AC: 6 AN: 19688

GnomAD4 genome AF: 0.000165 AC: 22 AN: 133728 Hom.: 1 Cov.: 20 AF XY: 0.000265 AC XY: 17 AN XY: 64082

African (AFR) AF: 0.00 AC: 0 AN: 34538

American (AMR) AF: 0.00 AC: 0 AN: 13020

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3314

East Asian (EAS) AF: 0.000425 AC: 2 AN: 4710

South Asian (SAS) AF: 0.00 AC: 0 AN: 3846

European-Finnish (FIN) AF: 0.00157 AC: 12 AN: 7620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 266

European-Non Finnish (NFE) AF: 0.000110 AC: 7 AN: 63718

Other (OTH) AF: 0.000545 AC: 1 AN: 1836

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	-0.91
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.21
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: rs369579197; hg19: chr3-188242697;