6-46704715-TAATC-TAATCAATC

Variant names:

• chr6-46704715-T-TAATC
• rs148052037
• NM_005084.4:c.1190-23_1190-20dupGATT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_005084.4(PLA2G7):​c.1190-23_1190-20dupGATT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. There are indicators that this mutation may affect the branch point..

• Frequency: Genomes: not found (cov: 18)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

Genes affected

PLA2G7 (HGNC:9040): (phospholipase A2 group VII) The protein encoded by this gene is a secreted enzyme that catalyzes the degradation of platelet-activating factor to biologically inactive products. Defects in this gene are a cause of platelet-activating factor acetylhydrolase deficiency. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.1190-23_1190-20dupGATT		intron_variant	Intron 11 of 11	ENST00000274793.12	NP_005075.3
PLA2G7	NM_001168357.2	c.1190-23_1190-20dupGATT		intron_variant	Intron 11 of 11		NP_001161829.1
PLA2G7	XM_005249408.5	c.1190-23_1190-20dupGATT		intron_variant	Intron 11 of 11		XP_005249465.1
PLA2G7	XM_047419359.1	c.1055-23_1055-20dupGATT		intron_variant	Intron 10 of 10		XP_047275315.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000274793.12	c.1190-20_1190-19insGATT		intron_variant	Intron 11 of 11	1	NM_005084.4	ENSP00000274793.7
PLA2G7	ENST00000537365.1	c.1190-20_1190-19insGATT		intron_variant	Intron 11 of 11	1		ENSP00000445666.1

Frequencies

GnomAD3 genomes Cov.: 18

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 18

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BranchPoint Hunter		5.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs148052037; hg19: chr6-46672452;