rs2886271

Variant names:

• chr12-6625147-C-T
• rs2886271
• NM_020400.6:c.-216-3683G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

ENSG00000301109 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LPAR5	NM_020400.6	c.-216-3683G>A		intron_variant	Intron 1 of 1	ENST00000329858.9	NP_065133.1
LPAR5	NM_001142961.1	c.-216-3683G>A		intron_variant	Intron 1 of 1		NP_001136433.1
LOC105369631	XR_007063192.1	n.659-1542C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAR5	ENST00000329858.9	c.-216-3683G>A		intron_variant	Intron 1 of 1	1	NM_020400.6	ENSP00000327875.4

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

African (AFR) AF: 0.430 AC: 17768 AN: 41316

American (AMR) AF: 0.125 AC: 1891 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3466

East Asian (EAS) AF: 0.00353 AC: 18 AN: 5102

South Asian (SAS) AF: 0.147 AC: 698 AN: 4738

European-Finnish (FIN) AF: 0.156 AC: 1647 AN: 10524

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10790 AN: 67924

Other (OTH) AF: 0.190 AC: 399 AN: 2104

Alfa AF: 0.172 Hom.: 4495

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
PhyloP100		-0.82
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: rs2886271; hg19: chr12-6734313;