rs1983853

chr1-84845509-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LPAR3	NM_012152.3	c.736+19876G>A		intron_variant		ENST00000370611.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LPAR3	ENST00000370611.4	c.736+19876G>A		intron_variant		1	NM_012152.3	P1
LPAR3	ENST00000440886.1	c.736+19876G>A		intron_variant		1		P1
LPAR3	ENST00000491034.1	n.615+19876G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0541

Gnomad4 AMR AF: 0.0868

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0876

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.110

Alfa AF: 0.118 Hom.: 1917

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1983853; hg19: chr1-85311192;