19-48053756-G-A

Variant names:

• chr19-48053756-G-A
• rs2162886
• NM_003706.3:c.1430-609C>T

Variant summary

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

The NM_003706.3(PLA2G4C):​c.1430-609C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,004 control chromosomes in the GnomAD database, including 29,791 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 0.61 (29791 hom., cov: 31)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 3 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Variant Effect in Transcripts

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

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4C	NM_003706.3	MANE Select	c.1430-609C>T		intron	N/A	NP_003697.2	Q9UP65-1
	PLA2G4C	NM_001159322.2		c.1460-609C>T		intron	N/A	NP_001152794.1	Q9UP65-3
	PLA2G4C	NM_001159323.2		c.1430-609C>T		intron	N/A	NP_001152795.1	Q9UP65-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4C	ENST00000599921.6	TSL:1 MANE Select	c.1430-609C>T		intron	N/A	ENSP00000469473.1	Q9UP65-1
	PLA2G4C	ENST00000594790.1	TSL:1	n.183-609C>T		intron	N/A
	PLA2G4C	ENST00000887096.1		c.1487-609C>T		intron	N/A	ENSP00000557155.1

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92836 AN: 151886 Hom.: 29777 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.611 AC: 92875 AN: 152004 Hom.: 29791 Cov.: 31 AF XY: 0.614 AC XY: 45629 AN XY: 74328

African (AFR) AF: 0.408 AC: 16893 AN: 41416

American (AMR) AF: 0.659 AC: 10046 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2056 AN: 3468

East Asian (EAS) AF: 0.903 AC: 4674 AN: 5176

South Asian (SAS) AF: 0.707 AC: 3408 AN: 4818

European-Finnish (FIN) AF: 0.696 AC: 7364 AN: 10586

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.681 AC: 46277 AN: 67992

Other (OTH) AF: 0.631 AC: 1331 AN: 2110

Alfa AF: 0.659 Hom.: 142966

Bravo AF: 0.600

Asia WGS AF: 0.781 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.2
DANN	Benign	0.80
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: rs2162886; hg19: chr19-48557013;