rs2886271

Positions:

• chr12-6625147-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020400.6(LPAR5):​c.-216-3683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 151,538 control chromosomes in the GnomAD database, including 5,081 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 0.22 (5081 hom., cov: 31)
• Consequence: LPAR5 NM_020400.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823

Genes affected

LPAR5 (HGNC:13307): (lysophosphatidic acid receptor 5) This gene encodes a member of the rhodopsin class of G protein-coupled transmembrane receptors. This protein transmits extracellular signals from lysophosphatidic acid to cells through heterotrimeric G proteins and mediates numerous cellular processes. Many G protein receptors serve as targets for pharmaceutical drugs. Transcript variants of this gene have been described.[provided by RefSeq, Dec 2008]

LPAR5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPAR5	NM_020400.6	c.-216-3683G>A		intron_variant		ENST00000329858.9	NP_065133.1
LPAR5	NM_001142961.1	c.-216-3683G>A		intron_variant			NP_001136433.1
LOC105369631	XR_007063192.1	n.659-1542C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPAR5	ENST00000329858.9	c.-216-3683G>A		intron_variant		1	NM_020400.6	ENSP00000327875.4
LPAR5	ENST00000431922.1	c.-216-3683G>A		intron_variant		2		ENSP00000393098.1
LPAR5	ENST00000540335.1	n.142-3683G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33668 AN: 151418 Hom.: 5069 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00352

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.222 AC: 33712 AN: 151538 Hom.: 5081 Cov.: 31 AF XY: 0.218 AC XY: 16123 AN XY: 74052

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.00353

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.190

Alfa AF: 0.164 Hom.: 3111

Bravo AF: 0.228

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.068
DANN	Benign	0.74

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: rs2886271; hg19: chr12-6734313;