rs1007000

Variant names:

• chr9-110900401-C-T
• rs1007000
• NM_001351411.2:c.794-24679G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LPAR1	NM_001351411.2	c.794-24679G>A		intron_variant	Intron 5 of 5	ENST00000683809.1	NP_001338340.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAR1	ENST00000683809.1	c.794-24679G>A		intron_variant	Intron 5 of 5		NM_001351411.2	ENSP00000506912.1
LPAR1	ENST00000374430.6	c.794-24679G>A		intron_variant	Intron 4 of 4	1		ENSP00000363552.1
LPAR1	ENST00000374431.7	c.794-24679G>A		intron_variant	Intron 4 of 4	1		ENSP00000363553.3
LPAR1	ENST00000358883.8	c.794-24679G>A		intron_variant	Intron 3 of 3	2		ENSP00000351755.4

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

African (AFR) AF: 0.0429 AC: 1779 AN: 41468

American (AMR) AF: 0.243 AC: 3705 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1029 AN: 5170

South Asian (SAS) AF: 0.225 AC: 1079 AN: 4802

European-Finnish (FIN) AF: 0.165 AC: 1748 AN: 10562

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14392 AN: 67952

Other (OTH) AF: 0.175 AC: 369 AN: 2114

Alfa AF: 0.199 Hom.: 13665

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
PhyloP100		-0.61
Mutation Taster		=100/0	polymorphism (auto)

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: rs1007000; hg19: chr9-113662681;