19-48073964-TTTTAATTTAA-TTTTAA

Variant names:

• chr19-48073964-TTTTAA-T
• rs11564612
• NM_003706.3:c.1006+798_1006+802delTTAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_003706.3(PLA2G4C):​c.1006+798_1006+802delTTAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00243 in 152,016 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0024 (1 hom., cov: 31)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 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: Uncertain_significance. The variant received 0 ACMG points.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4C	NM_003706.3	MANE Select	c.1006+798_1006+802delTTAAA		intron	N/A	NP_003697.2
	PLA2G4C	NM_001159322.2		c.1036+798_1036+802delTTAAA		intron	N/A	NP_001152794.1
	PLA2G4C	NM_001159323.2		c.1006+798_1006+802delTTAAA		intron	N/A	NP_001152795.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLA2G4C	ENST00000599921.6	TSL:1 MANE Select	c.1006+798_1006+802delTTAAA		intron	N/A	ENSP00000469473.1
	PLA2G4C	ENST00000595161.5	TSL:3	c.70+798_70+802delTTAAA		intron	N/A	ENSP00000469528.1
	PLA2G4C	ENST00000599111.5	TSL:2	c.1036+798_1036+802delTTAAA		intron	N/A	ENSP00000472546.1

Frequencies

GnomAD3 genomes AF: 0.00242 AC: 368 AN: 151898 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000847

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00144

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00385

Gnomad OTH AF: 0.00239

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

GnomAD4 genome AF: 0.00243 AC: 369 AN: 152016 Hom.: 1 Cov.: 31 AF XY: 0.00248 AC XY: 184 AN XY: 74338

African (AFR) AF: 0.000845 AC: 35 AN: 41426

American (AMR) AF: 0.00144 AC: 22 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00231 AC: 8 AN: 3464

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5162

South Asian (SAS) AF: 0.00519 AC: 25 AN: 4818

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00385 AC: 262 AN: 67964

Other (OTH) AF: 0.00237 AC: 5 AN: 2112

Alfa AF: 0.000547 Hom.: 0

Bravo AF: 0.00232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11564612; hg19: chr19-48577221;