19-48062095-C-A

Variant names:

• chr19-48062095-C-A
• rs201127134
• NM_003706.3:c.1160G>T
• PLA2G4C p.Gly387Val

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+1 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 1 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateB3_Supporting

The NM_003706.3(PLA2G4C):c.1160G>T (p.Gly387Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.G387A: Uncertain_significance (ClinVar VariationId 2376460, 1 star); p.G387S: Uncertain_significance (ClinVar VariationId 4138261, 1 star)

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLA2G4C NM_003706.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 0 publications found

Genes affected

PLA2G4C (HGNC:9037): (phospholipase A2 group IVC) This gene encodes a protein which is a member of the phospholipase A2 enzyme family which hydrolyzes glycerophospholipids to produce free fatty acids and lysophospholipids, both of which serve as precursors in the production of signaling molecules. The encoded protein has been shown to be a calcium-independent and membrane bound enzyme. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2009]

PLA2G4C-AS1 (HGNC:51585): ()

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 1 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])
	B3Computational evidence does not support deleterious effect		Computational evidence does not support a deleterious effect; Missense variant — primary computational scorer does not support an oncogenic/deleterious effect; supports B3

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_003706.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	PLA2G4C NM_003706.3	MANE Select	c.1160G>T p.Gly387Val	missense	Exon 14 of 17	Prot: NP_003697.2 UniProt:
	PLA2G4C NM_001159322.2		c.1190G>T p.Gly397Val	missense	Exon 14 of 17	Prot: NP_001152794.1 UniProt:
	PLA2G4C NM_001159323.2		c.1160G>T p.Gly387Val	missense	Exon 14 of 17	Prot: NP_001152795.1 UniProt:

PLA2G4C NM_003706.3

MANE Select

HGVSc / HGVSpc.1160G>Tp.Gly387Val

Exon rankExon 14 of 17

missense

Prot: NP_003697.2UniProt: Q9UP65-1

PLA2G4C NM_001159322.2

HGVSc / HGVSpc.1190G>Tp.Gly397Val

Exon rankExon 14 of 17

missense

Prot: NP_001152794.1UniProt: Q9UP65-3

PLA2G4C NM_001159323.2

HGVSc / HGVSpc.1160G>Tp.Gly387Val

Exon rankExon 14 of 17

missense

Prot: NP_001152795.1UniProt: Q9UP65-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	PLA2G4C ENST00000599921.6	TSL:1MANE Select	c.1160G>T p.Gly387Val	missense	Exon 14 of 17	Prot: ENSP00000469473.1 UniProt:
	PLA2G4C ENST00000595161.5	TSL:3	c.224G>T p.Gly75Val	missense	Exon 3 of 5	Prot: ENSP00000469528.1 UniProt:
	PLA2G4C ENST00000887096.1		c.1217G>T p.Gly406Val	missense	Exon 15 of 18	Prot: ENSP00000557155.1 UniProt:

PLA2G4C ENST00000599921.6

TSL:1MANE Select

HGVSc / HGVSpc.1160G>Tp.Gly387Val

Exon rankExon 14 of 17

missense

Prot: ENSP00000469473.1UniProt: Q9UP65-1

PLA2G4C ENST00000595161.5

TSL:3

HGVSc / HGVSpc.224G>Tp.Gly75Val

Exon rankExon 3 of 5

missense

Prot: ENSP00000469528.1UniProt: M0QY18

PLA2G4C ENST00000887096.1

HGVSc / HGVSpc.1217G>Tp.Gly406Val

Exon rankExon 15 of 18

missense

Prot: ENSP00000557155.1UniProt: A0ACI8QRI2

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:31
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 3 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	24
AlphaMissense	Pathogenic	0.93
BayesDel_addAF	Uncertain	0.098	D
BayesDel_noAF	Benign	-0.10
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.35	T
Eigen	Uncertain	0.27
Eigen_PC	Benign	0.089
FATHMM_MKL	Benign	0.29	N
FuncVEP CTI	Pathogenic	0.99
GPN-Star LLR	N/A	-5.0
GPN-Star score	N/A	5.0
LIST_S2	Benign	0.80	T
M_CAP	Benign	0.018	T
MetaRNN	Pathogenic	0.89	D
MetaSVM	Benign	-0.94	T
Mutation Taster	N/A	84/16	polymorphism
MutationAssessor	Pathogenic	3.2	M
PhyloP100	Benign	1.6
popEVE	Benign	-3.9
PrimateAI	Uncertain	0.50	T
PROVEAN	Pathogenic	-7.3	D
REVEL	Benign	0.26
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0050	D
Varity_R	N/A	0.61
VESM-3B	Benign	-14

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs201127134;

hg19: chr19-48565352;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar