rs3741924

Variant names:

• chr12-6620790-G-A
• rs3741924
• NM_020400.6:c.459C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-6620790-G-A
• chr12-6620790-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BS1 BS2

The NM_020400.6(LPAR5):​c.459C>T​(p.Ala153Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 1,580,442 control chromosomes in the GnomAD database, including 350 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 0.013 (27 hom., cov: 32)
  • Exomes 𝑓: 0.019 (323 hom.)
• Consequence: LPAR5 NM_020400.6 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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]

LOC105369631 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BP7: Synonymous conserved (PhyloP=-0.658 with no splicing effect.
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0133 (2020/152342) while in subpopulation EAS AF= 0.0216 (112/5182). AF 95% confidence interval is 0.0193. There are 27 homozygotes in gnomad4. There are 930 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 27 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LPAR5	NM_020400.6	c.459C>T	p.Ala153Ala	synonymous_variant	Exon 2 of 2	ENST00000329858.9	NP_065133.1
LPAR5	NM_001142961.1	c.459C>T	p.Ala153Ala	synonymous_variant	Exon 2 of 2		NP_001136433.1
LOC105369631	XR_007063192.1	n.658+3001G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LPAR5	ENST00000329858.9	c.459C>T	p.Ala153Ala	synonymous_variant	Exon 2 of 2	1	NM_020400.6	ENSP00000327875.4
LPAR5	ENST00000431922.1	c.459C>T	p.Ala153Ala	synonymous_variant	Exon 2 of 2	2		ENSP00000393098.1
LPAR5	ENST00000540335.1	n.816C>T		non_coding_transcript_exon_variant	Exon 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0133 AC: 2022 AN: 152224 Hom.: 27 Cov.: 32

Gnomad AFR AF: 0.00357

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0107

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.0216

Gnomad SAS AF: 0.00434

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0139

GnomAD3 exomes AF: 0.0138 AC: 2567 AN: 185374 Hom.: 31 AF XY: 0.0135 AC XY: 1384 AN XY: 102556

Gnomad AFR exome AF: 0.00241

Gnomad AMR exome AF: 0.00492

Gnomad ASJ exome AF: 0.00286

Gnomad EAS exome AF: 0.0250

Gnomad SAS exome AF: 0.00508

Gnomad FIN exome AF: 0.0139

Gnomad NFE exome AF: 0.0206

Gnomad OTH exome AF: 0.0135

GnomAD4 exome AF: 0.0195 AC: 27842 AN: 1428100 Hom.: 323 Cov.: 31 AF XY: 0.0189 AC XY: 13411 AN XY: 707792

Gnomad4 AFR exome AF: 0.00256

Gnomad4 AMR exome AF: 0.00584

Gnomad4 ASJ exome AF: 0.00258

Gnomad4 EAS exome AF: 0.0327

Gnomad4 SAS exome AF: 0.00483

Gnomad4 FIN exome AF: 0.0148

Gnomad4 NFE exome AF: 0.0219

Gnomad4 OTH exome AF: 0.0177

GnomAD4 genome AF: 0.0133 AC: 2020 AN: 152342 Hom.: 27 Cov.: 32 AF XY: 0.0125 AC XY: 930 AN XY: 74506

Gnomad4 AFR AF: 0.00356

Gnomad4 AMR AF: 0.0107

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.00414

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0157 Hom.: 11

Bravo AF: 0.0134

Asia WGS AF: 0.00636 AC: 22 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.8
DANN	Benign	0.95
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs3741924; hg19: chr12-6729956;