rs2805386

chr9-110919720-A-Gchr9-110919720-A-T

Variant summary

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

The NM_001351411.2(LPAR1):c.793+21701T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,086 control chromosomes in the GnomAD database, including 9,673 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 (9673 hom., cov: 32)
• Consequence: LPAR1 NM_001351411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LPAR1	NM_001351411.2	c.793+21701T>C		intron_variant		ENST00000683809.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPAR1	ENST00000683809.1	c.793+21701T>C		intron_variant			NM_001351411.2	P1
LPAR1	ENST00000374430.6	c.793+21701T>C		intron_variant		1		P1
LPAR1	ENST00000374431.7	c.793+21701T>C		intron_variant		1		P1
LPAR1	ENST00000358883.8	c.793+21701T>C		intron_variant		2		P1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50867 AN: 151966 Hom.: 9674 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.0318

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.335 AC: 50879 AN: 152086 Hom.: 9673 Cov.: 32 AF XY: 0.330 AC XY: 24518 AN XY: 74344

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.342

Alfa AF: 0.356 Hom.: 1771

Bravo AF: 0.315

Asia WGS AF: 0.144 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.3
Dann	Benign	0.48

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: rs2805386; hg19: chr9-113682000;