chr9-110977358-A-G

Position:

• chr9-110977358-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351411.2(LPAR1):​c.-181-3800T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,982 control chromosomes in the GnomAD database, including 9,452 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 0.33 (9452 hom., cov: 31)
• Consequence: LPAR1 NM_001351411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420

Genes affected

LPAR1 (HGNC:3166): (lysophosphatidic acid receptor 1) The integral membrane protein encoded by this gene is a lysophosphatidic acid (LPA) receptor from a group known as EDG receptors. These receptors are members of the G protein-coupled receptor superfamily. Utilized by LPA for cell signaling, EDG receptors mediate diverse biologic functions, including proliferation, platelet aggregation, smooth muscle contraction, inhibition of neuroblastoma cell differentiation, chemotaxis, and tumor cell invasion. Many transcript variants encoding a few different isoforms have been identified for this gene. [provided by RefSeq, Oct 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPAR1	NM_001351411.2	c.-181-3800T>C		intron_variant		ENST00000683809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPAR1	ENST00000683809.1	c.-181-3800T>C		intron_variant			NM_001351411.2	P1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50711 AN: 151864 Hom.: 9450 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.349

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.334 AC: 50709 AN: 151982 Hom.: 9452 Cov.: 31 AF XY: 0.327 AC XY: 24260 AN XY: 74274

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.00252

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.425

Gnomad4 OTH AF: 0.341

Alfa AF: 0.394 Hom.: 7095

Bravo AF: 0.321

Asia WGS AF: 0.105 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.54

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

Publications

LitVar

Other links and lift over

dbSNP: rs4366150; hg19: chr9-113739638;