19-48077996-C-G

Variant names:

• chr19-48077996-C-G
• rs1019785
• NM_003706.3:c.845-172G>C

Variant summary

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

The NM_003706.3(PLA2G4C):​c.845-172G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,200 control chromosomes in the GnomAD database, including 65,051 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 0.92 (65051 hom., cov: 32)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 2 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.845-172G>C		intron_variant	Intron 10 of 16	ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.845-172G>C		intron_variant	Intron 10 of 16	1	NM_003706.3	ENSP00000469473.1

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140030 AN: 152082 Hom.: 65009 Cov.: 32

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.969

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.921 AC: 140129 AN: 152200 Hom.: 65051 Cov.: 32 AF XY: 0.924 AC XY: 68746 AN XY: 74416

African (AFR) AF: 0.794 AC: 32955 AN: 41484

American (AMR) AF: 0.956 AC: 14594 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.938 AC: 3258 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5134 AN: 5182

South Asian (SAS) AF: 0.951 AC: 4587 AN: 4824

European-Finnish (FIN) AF: 0.995 AC: 10559 AN: 10616

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.969 AC: 65941 AN: 68032

Other (OTH) AF: 0.933 AC: 1973 AN: 2114

Alfa AF: 0.945 Hom.: 7957

Bravo AF: 0.911

Asia WGS AF: 0.968 AC: 3366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.43
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1019785; hg19: chr19-48581253;