rs17688076

chr16-68252524-C-A

Variant summary

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

The NM_012320.4(PLA2G15):c.285-2395C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 455,970 control chromosomes in the GnomAD database, including 4,279 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 0.11 (1005 hom., cov: 32)
  • Exomes 𝑓: 0.14 (3274 hom.)
• Consequence: PLA2G15 NM_012320.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

PLA2G15 (HGNC:17163): (phospholipase A2 group XV) Lysophospholipases are enzymes that act on biological membranes to regulate the multifunctional lysophospholipids. The protein encoded by this gene hydrolyzes lysophosphatidylcholine to glycerophosphorylcholine and a free fatty acid. This enzyme is present in the plasma and thought to be associated with high-density lipoprotein. A later paper contradicts the function of this gene. It demonstrates that this gene encodes a lysosomal enzyme instead of a lysophospholipase and has both calcium-independent phospholipase A2 and transacylase activities. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G15	NM_012320.4	c.285-2395C>A		intron_variant		ENST00000219345.10
PLA2G15	NM_001363551.2	c.285-2395C>A		intron_variant
PLA2G15	XM_011522979.3	c.285-898C>A		intron_variant
PLA2G15	XM_011522980.4	c.285-898C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G15	ENST00000219345.10	c.285-2395C>A		intron_variant		1	NM_012320.4	P1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16481 AN: 152142 Hom.: 1001 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.123

GnomAD3 exomes AF: 0.139 AC: 17820 AN: 127854 Hom.: 1385 AF XY: 0.142 AC XY: 9909 AN XY: 69956

Gnomad AFR exome AF: 0.0604

Gnomad AMR exome AF: 0.149

Gnomad ASJ exome AF: 0.161

Gnomad EAS exome AF: 0.111

Gnomad SAS exome AF: 0.203

Gnomad FIN exome AF: 0.145

Gnomad NFE exome AF: 0.117

Gnomad OTH exome AF: 0.134

GnomAD4 exome AF: 0.138 AC: 42046 AN: 303710 Hom.: 3274 Cov.: 0 AF XY: 0.143 AC XY: 24800 AN XY: 172956

Gnomad4 AFR exome AF: 0.0606

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.163

Gnomad4 EAS exome AF: 0.115

Gnomad4 SAS exome AF: 0.200

Gnomad4 FIN exome AF: 0.147

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.127

GnomAD4 genome AF: 0.108 AC: 16504 AN: 152260 Hom.: 1005 Cov.: 32 AF XY: 0.113 AC XY: 8444 AN XY: 74426

Gnomad4 AFR AF: 0.0629

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.114

Gnomad4 OTH AF: 0.127

Alfa AF: 0.116 Hom.: 200

Bravo AF: 0.105

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	1.1
Dann	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17688076; hg19: chr16-68286427; COSMIC: COSV54723276; COSMIC: COSV54723276;