rs1536435

Variant names:

• chr9-110886559-A-G
• rs1536435
• NM_001351411.2:c.794-10837T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-110886559-A-G
• chr9-110886559-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.794-10837T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,020 control chromosomes in the GnomAD database, including 26,396 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 0.57 (26396 hom., cov: 32)
• Consequence: LPAR1 NM_001351411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.428
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351411.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAR1	NM_001351411.2	MANE Select	c.794-10837T>C		intron	N/A	NP_001338340.1	Q92633-1
	LPAR1	NM_001351397.2		c.794-10837T>C		intron	N/A	NP_001338326.1	Q92633-1
	LPAR1	NM_001351398.2		c.794-10837T>C		intron	N/A	NP_001338327.1	Q92633-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAR1	ENST00000683809.1	MANE Select	c.794-10837T>C		intron	N/A	ENSP00000506912.1	Q92633-1
	LPAR1	ENST00000374430.6	TSL:1	c.794-10837T>C		intron	N/A	ENSP00000363552.1	Q92633-1
	LPAR1	ENST00000374431.7	TSL:1	c.794-10837T>C		intron	N/A	ENSP00000363553.3	Q92633-1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86660 AN: 151902 Hom.: 26362 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.571 AC: 86740 AN: 152020 Hom.: 26396 Cov.: 32 AF XY: 0.565 AC XY: 41987 AN XY: 74328

African (AFR) AF: 0.726 AC: 30079 AN: 41458

American (AMR) AF: 0.461 AC: 7031 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1959 AN: 3470

East Asian (EAS) AF: 0.0660 AC: 342 AN: 5182

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4822

European-Finnish (FIN) AF: 0.614 AC: 6486 AN: 10560

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37240 AN: 67948

Other (OTH) AF: 0.546 AC: 1153 AN: 2110

Alfa AF: 0.544 Hom.: 29163

Bravo AF: 0.562

Asia WGS AF: 0.274 AC: 953 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.70
PhyloP100		-0.43
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: rs1536435; hg19: chr9-113648839;