rs1007000

Positions:

• chr9-110900401-C-T

Variant summary

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

The NM_001351411.2(LPAR1):​c.794-24679G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,008 control chromosomes in the GnomAD database, including 2,593 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 0.16 (2593 hom., cov: 32)
• Consequence: LPAR1 NM_001351411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPAR1	NM_001351411.2	c.794-24679G>A		intron_variant		ENST00000683809.1	NP_001338340.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPAR1	ENST00000683809.1	c.794-24679G>A		intron_variant			NM_001351411.2	ENSP00000506912	P1
LPAR1	ENST00000374430.6	c.794-24679G>A		intron_variant		1		ENSP00000363552	P1
LPAR1	ENST00000374431.7	c.794-24679G>A		intron_variant		1		ENSP00000363553	P1
LPAR1	ENST00000358883.8	c.794-24679G>A		intron_variant		2		ENSP00000351755	P1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24812 AN: 151890 Hom.: 2588 Cov.: 32

Gnomad AFR AF: 0.0431

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.163 AC: 24833 AN: 152008 Hom.: 2593 Cov.: 32 AF XY: 0.164 AC XY: 12169 AN XY: 74282

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.175

Alfa AF: 0.207 Hom.: 6979

Bravo AF: 0.165

Asia WGS AF: 0.209 AC: 730 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	1.2
DANN	Benign	0.65

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: rs1007000; hg19: chr9-113662681;