chr1-84824726-T-C

Variant names:

• chr1-84824726-T-C
• rs9728717
• NM_012152.3:c.737-10555A>G

Variant summary

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

The NM_012152.3(LPAR3):​c.737-10555A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,134 control chromosomes in the GnomAD database, including 5,181 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 0.24 (5181 hom., cov: 32)
• Consequence: LPAR3 NM_012152.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 8 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAR3	NM_012152.3	MANE Select	c.737-10555A>G		intron	N/A	NP_036284.1	Q9UBY5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LPAR3	ENST00000370611.4	TSL:1 MANE Select	c.737-10555A>G		intron	N/A	ENSP00000359643.3	Q9UBY5
	LPAR3	ENST00000440886.1	TSL:1	c.737-10555A>G		intron	N/A	ENSP00000395389.1	Q9UBY5
	LPAR3	ENST00000930963.1		c.737-10555A>G		intron	N/A	ENSP00000601022.1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36043 AN: 152016 Hom.: 5173 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.237 AC: 36079 AN: 152134 Hom.: 5181 Cov.: 32 AF XY: 0.232 AC XY: 17258 AN XY: 74382

African (AFR) AF: 0.399 AC: 16541 AN: 41468

American (AMR) AF: 0.193 AC: 2956 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 623 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5178

South Asian (SAS) AF: 0.131 AC: 634 AN: 4826

European-Finnish (FIN) AF: 0.146 AC: 1546 AN: 10604

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13103 AN: 67980

Other (OTH) AF: 0.243 AC: 514 AN: 2116

Alfa AF: 0.208 Hom.: 11473

Bravo AF: 0.249

Asia WGS AF: 0.0840 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		1.1
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: rs9728717; hg19: chr1-85290409;