rs1983853

Variant names:

• chr1-84845509-C-T
• rs1983853
• NM_012152.3:c.736+19876G>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+19876G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,202 control chromosomes in the GnomAD database, including 819 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 0.097 (819 hom., cov: 32)
• Consequence: LPAR3 NM_012152.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 21 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPAR3	NM_012152.3	c.736+19876G>A		intron_variant	Intron 2 of 2	ENST00000370611.4	NP_036284.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAR3	ENST00000370611.4	c.736+19876G>A		intron_variant	Intron 2 of 2	1	NM_012152.3	ENSP00000359643.3
LPAR3	ENST00000440886.1	c.736+19876G>A		intron_variant	Intron 1 of 1	1		ENSP00000395389.1
LPAR3	ENST00000491034.1	n.615+19876G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14770 AN: 152082 Hom.: 819 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0875

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.0971 AC: 14772 AN: 152202 Hom.: 819 Cov.: 32 AF XY: 0.0956 AC XY: 7114 AN XY: 74408

African (AFR) AF: 0.0541 AC: 2246 AN: 41538

American (AMR) AF: 0.0868 AC: 1326 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5178

South Asian (SAS) AF: 0.0876 AC: 422 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10588

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8362 AN: 68008

Other (OTH) AF: 0.110 AC: 232 AN: 2112

Alfa AF: 0.113 Hom.: 2688

Bravo AF: 0.0949

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.9
DANN	Benign	0.54
PhyloP100		0.18
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: rs1983853; hg19: chr1-85311192;