chr9-110994184-T-C

Position:

• chr9-110994184-T-C

Variant summary

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

The NM_001351411.2(LPAR1):​c.-181-20626A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,980 control chromosomes in the GnomAD database, including 7,658 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 0.32 (7658 hom., cov: 32)
• Consequence: LPAR1 NM_001351411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPAR1	NM_001351411.2	c.-181-20626A>G		intron_variant		ENST00000683809.1	NP_001338340.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPAR1	ENST00000683809.1	c.-181-20626A>G		intron_variant			NM_001351411.2	ENSP00000506912	P1

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47969 AN: 151862 Hom.: 7655 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.316 AC: 48024 AN: 151980 Hom.: 7658 Cov.: 32 AF XY: 0.311 AC XY: 23098 AN XY: 74272

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.292

Alfa AF: 0.332 Hom.: 1438

Bravo AF: 0.322

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.51

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: rs10980684; hg19: chr9-113756464;