rs11728699

chr4-109728735-G-T

Variant summary

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

The NM_030821.5(PLA2G12A):c.208+867C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,096 control chromosomes in the GnomAD database, including 30,716 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 0.62 (30716 hom., cov: 32)
• Consequence: PLA2G12A NM_030821.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

Genes affected

PLA2G12A (HGNC:18554): (phospholipase A2 group XIIA) Secreted phospholipase A2 (sPLA2) enzymes liberate arachidonic acid from phospholipids for production of eicosanoids and exert a variety of physiologic and pathologic effects. Group XII sPLA2s, such as PLA2G12A, have relatively low specific activity and are structurally and functionally distinct from other sPLA2s (Gelb et al., 2000 [PubMed 11031251]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -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 = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G12A	NM_030821.5	c.208+867C>A		intron_variant		ENST00000243501.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G12A	ENST00000243501.10	c.208+867C>A		intron_variant		1	NM_030821.5	P3
PLA2G12A	ENST00000502283.1	c.208+867C>A		intron_variant		1		A1
PLA2G12A	ENST00000507961.1	c.208+867C>A		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94522 AN: 151978 Hom.: 30655 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.622 AC: 94644 AN: 152096 Hom.: 30716 Cov.: 32 AF XY: 0.615 AC XY: 45722 AN XY: 74350

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.582

Alfa AF: 0.584 Hom.: 9026

Bravo AF: 0.627

Asia WGS AF: 0.517 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	3.3
Dann	Benign	0.76

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: rs11728699; hg19: chr4-110649891;