rs3087494

chr4-109710465-A-Gchr4-109710465-A-T

Variant summary

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

The NM_030821.5(PLA2G12A):c.*3912T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 152,084 control chromosomes in the GnomAD database, including 18,773 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 0.49 (18773 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: PLA2G12A NM_030821.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.976

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLA2G12A	NM_030821.5	c.*3912T>C		3_prime_UTR_variant	4/4	ENST00000243501.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLA2G12A	ENST00000243501.10	c.*3912T>C		3_prime_UTR_variant	4/4	1	NM_030821.5	P3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74327 AN: 151966 Hom.: 18762 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.491

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.489 AC: 74370 AN: 152084 Hom.: 18773 Cov.: 33 AF XY: 0.491 AC XY: 36496 AN XY: 74354

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.490

Alfa AF: 0.536 Hom.: 35858

Bravo AF: 0.474

Asia WGS AF: 0.548 AC: 1903 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.47

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: rs3087494; hg19: chr4-110631621;