chr19-48073964-T-TTTTAA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_003706.3(PLA2G4C):​c.1006+798_1006+802dupTTAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00517 in 152,016 control chromosomes in the GnomAD database, including 6 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0052 (6 hom., cov: 31)
• Consequence: PLA2G4C NM_003706.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• 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: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00517 (786/152016) while in subpopulation AFR AF = 0.0175 (723/41424). AF 95% confidence interval is 0.0164. There are 6 homozygotes in GnomAd4. There are 363 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4C	NM_003706.3	c.1006+798_1006+802dupTTAAA		intron_variant	Intron 12 of 16	ENST00000599921.6	NP_003697.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4C	ENST00000599921.6	c.1006+802_1006+803insTTAAA		intron_variant	Intron 12 of 16	1	NM_003706.3	ENSP00000469473.1
PLA2G4C	ENST00000595161.5	c.70+802_70+803insTTAAA		intron_variant	Intron 1 of 4	3		ENSP00000469528.1

Frequencies

GnomAD3 genomes AF: 0.00515 AC: 783 AN: 151898 Hom.: 6 Cov.: 31

Gnomad AFR AF: 0.0174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00151

Gnomad ASJ AF: 0.000866

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000830

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.00335

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

GnomAD4 genome AF: 0.00517 AC: 786 AN: 152016 Hom.: 6 Cov.: 31 AF XY: 0.00488 AC XY: 363 AN XY: 74338

African (AFR) AF: 0.0175 AC: 723 AN: 41424

American (AMR) AF: 0.00151 AC: 23 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.000866 AC: 3 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5162

South Asian (SAS) AF: 0.000830 AC: 4 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

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

European-Non Finnish (NFE) AF: 0.000383 AC: 26 AN: 67966

Other (OTH) AF: 0.00331 AC: 7 AN: 2112

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.21

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;