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GeneBe

1-84865779-A-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_012152.3(LPAR3):c.342T>G(p.Thr114=) 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

2

Clinical Significance

Benign criteria provided, single submitter B:1

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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-3.36 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 1356 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LPAR3NM_012152.3 linkuse as main transcriptc.342T>G p.Thr114= synonymous_variant 2/3 ENST00000370611.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LPAR3ENST00000370611.4 linkuse as main transcriptc.342T>G p.Thr114= synonymous_variant 2/31 NM_012152.3 P1
LPAR3ENST00000440886.1 linkuse as main transcriptc.342T>G p.Thr114= synonymous_variant 1/21 P1
LPAR3ENST00000491034.1 linkuse as main transcriptn.366T>G non_coding_transcript_exon_variant 1/33

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00891
AC:
1356
AN:
152224
Hom.:
12
Cov.:
32
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.:
19
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.:
32
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00890
AC:
1356
AN:
152342
Hom.:
12
Cov.:
32
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.:
3
Bravo
AF:
0.00948
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.0130
EpiControl
AF:
0.0145

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJun 04, 2018- -

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.

Other links and lift over

dbSNP: rs41289037; hg19: chr1-85331462; API