rs2805386

Variant names:

• chr9-110919720-A-G
• rs2805386
• NM_001351411.2:c.793+21701T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-110919720-A-G
• chr9-110919720-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.84).
• 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 rank	MANE	Protein	UniProt
LPAR1	NM_001351411.2	c.793+21701T>C		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.793+21701T>C		intron_variant	Intron 5 of 5		NM_001351411.2	ENSP00000506912.1
LPAR1	ENST00000374430.6	c.793+21701T>C		intron_variant	Intron 4 of 4	1		ENSP00000363552.1
LPAR1	ENST00000374431.7	c.793+21701T>C		intron_variant	Intron 4 of 4	1		ENSP00000363553.3
LPAR1	ENST00000358883.8	c.793+21701T>C		intron_variant	Intron 3 of 3	2		ENSP00000351755.4

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

African (AFR) AF: 0.211 AC: 8760 AN: 41478

American (AMR) AF: 0.306 AC: 4670 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3470

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1028 AN: 4820

European-Finnish (FIN) AF: 0.422 AC: 4462 AN: 10584

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 28999 AN: 67958

Other (OTH) AF: 0.342 AC: 723 AN: 2112

Alfa AF: 0.352 Hom.: 1791

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
PhyloP100		0.57
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: rs2805386; hg19: chr9-113682000;