1-84851157-G-T

Variant names:

• chr1-84851157-G-T
• rs4907103
• NM_012152.3:c.736+14228C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012152.3(LPAR3):​c.736+14228C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,118 control chromosomes in the GnomAD database, including 18,652 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 0.49 (18652 hom., cov: 33)
• Consequence: LPAR3 NM_012152.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 1 publications found

Genes affected

LPAR3 (HGNC:14298): (lysophosphatidic acid receptor 3) This gene encodes a member of the G protein-coupled receptor family, as well as the EDG family of proteins. This protein functions as a cellular receptor for lysophosphatidic acid and mediates lysophosphatidic acid-evoked calcium mobilization. This receptor couples predominantly to G(q/11) alpha proteins. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012152.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAR3	NM_012152.3	MANE Select	c.736+14228C>A		intron	N/A	NP_036284.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAR3	ENST00000370611.4	TSL:1 MANE Select	c.736+14228C>A		intron	N/A	ENSP00000359643.3
	LPAR3	ENST00000440886.1	TSL:1	c.736+14228C>A		intron	N/A	ENSP00000395389.1
	LPAR3	ENST00000491034.1	TSL:3	n.615+14228C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75220 AN: 152000 Hom.: 18657 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.495 AC: 75241 AN: 152118 Hom.: 18652 Cov.: 33 AF XY: 0.495 AC XY: 36837 AN XY: 74358

African (AFR) AF: 0.478 AC: 19825 AN: 41486

American (AMR) AF: 0.437 AC: 6683 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1747 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2604 AN: 5184

South Asian (SAS) AF: 0.486 AC: 2344 AN: 4822

European-Finnish (FIN) AF: 0.548 AC: 5804 AN: 10582

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34772 AN: 67958

Other (OTH) AF: 0.464 AC: 981 AN: 2114

Alfa AF: 0.499 Hom.: 54334

Bravo AF: 0.486

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.74
DANN	Benign	0.52
PhyloP100		-0.093
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: rs4907103; hg19: chr1-85316840;