Variant chr1-84865779-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_012152.3(LPAR3):c.342T>G(p.Thr114Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 1,614,224 control chromosomes in the GnomAD database, including 148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0089 ( 12 hom., cov: 32)

Exomes 𝑓: 0.013 ( 136 hom. )

Consequence

LPAR3
NM_012152.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.36

Variant links:

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]

LPAR3 links:

LPAR3 (HGNC:):

LPAR3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 1-84865779-A-C is Benign according to our data. Variant chr1-84865779-A-C is described in ClinVar as [Benign]. Clinvar id is 717261.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.36 with no splicing effect.

BS2

High AC in GnomAd4 at 1356 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPAR3	NM_012152.3 linkuse as main transcript	c.342T>G	p.Thr114Thr	synonymous_variant	2/3	ENST00000370611.4	NP_036284.1	Q9UBY5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
LPAR3	ENST00000370611.4 linkuse as main transcript	c.342T>G	p.Thr114Thr	synonymous_variant	2/3	1	NM_012152.3	ENSP00000359643.3	Q9UBY5
LPAR3	ENST00000440886.1 linkuse as main transcript	c.342T>G	p.Thr114Thr	synonymous_variant	1/2	1		ENSP00000395389.1	Q9UBY5
LPAR3	ENST00000491034.1 linkuse as main transcript	n.366T>G		non_coding_transcript_exon_variant	1/3	3

Frequencies

GnomAD3 genomes

AF:

0.00891

AC:

1356

AN:

152224

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00311

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0106

Gnomad ASJ

AF:

0.00806

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00186

Gnomad FIN

AF:

0.00358

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0142

Gnomad OTH

AF:

0.0115

GnomAD3 exomes

AF:

0.00913

AC:

2294

AN:

251304

Hom.:

AF XY:

0.00870

AC XY:

1181

AN XY:

135806

show subpopulations

Gnomad AFR exome

AF:

0.00203

Gnomad AMR exome

AF:

0.0106

Gnomad ASJ exome

AF:

0.00943

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00216

Gnomad FIN exome

AF:

0.00430

Gnomad NFE exome

AF:

0.0139

Gnomad OTH exome

AF:

0.0106

GnomAD4 exome

AF:

0.0129

AC:

18802

AN:

1461882

Hom.:

136

Cov.:

AF XY:

0.0125

AC XY:

9103

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.00254

Gnomad4 AMR exome

AF:

0.0102

Gnomad4 ASJ exome

AF:

0.00872

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00255

Gnomad4 FIN exome

AF:

0.00507

Gnomad4 NFE exome

AF:

0.0151

Gnomad4 OTH exome

AF:

0.0111

GnomAD4 genome

AF:

0.00890

AC:

1356

AN:

152342

Hom.:

Cov.:

AF XY:

0.00844

AC XY:

629

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00310

Gnomad4 AMR

AF:

0.0106

Gnomad4 ASJ

AF:

0.00806

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00358

Gnomad4 NFE

AF:

0.0142

Gnomad4 OTH

AF:

0.0113

Alfa

AF:

0.00999

Hom.:

Bravo

AF:

0.00948

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0130

EpiControl

AF:

0.0145

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 04, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.021

DANN

Benign

0.30

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over