chr9-110933261-C-A

Variant names:

• chr9-110933261-C-A
• rs4538964
• NM_001351411.2:c.793+8160G>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+8160G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 151,974 control chromosomes in the GnomAD database, including 31,964 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 0.63 (31964 hom., cov: 31)
• Consequence: LPAR1 NM_001351411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPAR1	NM_001351411.2	c.793+8160G>T		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+8160G>T		intron_variant	Intron 5 of 5		NM_001351411.2	ENSP00000506912.1
LPAR1	ENST00000374430.6	c.793+8160G>T		intron_variant	Intron 4 of 4	1		ENSP00000363552.1
LPAR1	ENST00000374431.7	c.793+8160G>T		intron_variant	Intron 4 of 4	1		ENSP00000363553.3
LPAR1	ENST00000358883.8	c.793+8160G>T		intron_variant	Intron 3 of 3	2		ENSP00000351755.4

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96237 AN: 151856 Hom.: 31912 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.634 AC: 96347 AN: 151974 Hom.: 31964 Cov.: 31 AF XY: 0.638 AC XY: 47361 AN XY: 74260

African (AFR) AF: 0.785 AC: 32548 AN: 41438

American (AMR) AF: 0.668 AC: 10206 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1685 AN: 3470

East Asian (EAS) AF: 0.969 AC: 4999 AN: 5160

South Asian (SAS) AF: 0.738 AC: 3540 AN: 4798

European-Finnish (FIN) AF: 0.531 AC: 5596 AN: 10536

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35641 AN: 67968

Other (OTH) AF: 0.629 AC: 1327 AN: 2110

Alfa AF: 0.560 Hom.: 12546

Bravo AF: 0.657

Asia WGS AF: 0.845 AC: 2936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		0.22
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: rs4538964; hg19: chr9-113695541;