rs8110925

Variant names:

• chr19-48060175-A-G
• rs8110925
• NM_003706.3:c.1257+1823T>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.1257+1823T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,104 control chromosomes in the GnomAD database, including 1,323 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 0.10 (1323 hom., cov: 30)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.1257+1823T>C		intron_variant	Intron 14 of 16	ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.1257+1823T>C		intron_variant	Intron 14 of 16	1	NM_003706.3	ENSP00000469473.1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15878 AN: 151986 Hom.: 1317 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0307

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.0605

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.105 AC: 15912 AN: 152104 Hom.: 1323 Cov.: 30 AF XY: 0.101 AC XY: 7507 AN XY: 74374

African (AFR) AF: 0.227 AC: 9395 AN: 41450

American (AMR) AF: 0.0926 AC: 1414 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0369 AC: 128 AN: 3472

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5174

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4828

European-Finnish (FIN) AF: 0.0623 AC: 661 AN: 10614

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0562 AC: 3818 AN: 67982

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0762 Hom.: 382

Bravo AF: 0.114

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.63
PhyloP100		0.22
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: rs8110925; hg19: chr19-48563432;