16-68251944-A-G

Variant names:

• chr16-68251944-A-G
• rs1975802
• NM_012320.4:c.284+2498A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012320.4(PLA2G15):​c.284+2498A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 150,518 control chromosomes in the GnomAD database, including 6,130 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 0.25 (6130 hom., cov: 31)
• Consequence: PLA2G15 NM_012320.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012320.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G15	NM_012320.4	MANE Select	c.284+2498A>G		intron	N/A	NP_036452.1
	PLA2G15	NM_001363551.2		c.284+2498A>G		intron	N/A	NP_001350480.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G15	ENST00000219345.10	TSL:1 MANE Select	c.284+2498A>G		intron	N/A	ENSP00000219345.5
	PLA2G15	ENST00000413021.2	TSL:2	c.128-2975A>G		intron	N/A	ENSP00000394197.2
	PLA2G15	ENST00000568082.1	TSL:5	c.284+2498A>G		intron	N/A	ENSP00000454557.1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38219 AN: 150422 Hom.: 6101 Cov.: 31

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.254 AC: 38302 AN: 150518 Hom.: 6130 Cov.: 31 AF XY: 0.256 AC XY: 18743 AN XY: 73340

African (AFR) AF: 0.451 AC: 18461 AN: 40952

American (AMR) AF: 0.218 AC: 3280 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3462

East Asian (EAS) AF: 0.108 AC: 549 AN: 5088

South Asian (SAS) AF: 0.262 AC: 1250 AN: 4766

European-Finnish (FIN) AF: 0.189 AC: 1904 AN: 10086

Middle Eastern (MID) AF: 0.318 AC: 91 AN: 286

European-Non Finnish (NFE) AF: 0.165 AC: 11171 AN: 67806

Other (OTH) AF: 0.259 AC: 540 AN: 2088

Alfa AF: 0.190 Hom.: 1610

Bravo AF: 0.262

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.34
PhyloP100		-1.1
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: rs1975802; hg19: chr16-68285847;