rs1362931

Variant names:

• chr6-46714342-A-C
• rs1362931
• NM_005084.4:c.470+118T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-46714342-A-C
• chr6-46714342-A-G
• chr6-46714342-A-T

Variant summary

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

The NM_005084.4(PLA2G7):​c.470+118T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 776,726 control chromosomes in the GnomAD database, including 262,576 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 0.83 (52800 hom., cov: 30)
  • Exomes 𝑓: 0.82 (209776 hom.)
• Consequence: PLA2G7 NM_005084.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G7	NM_005084.4	c.470+118T>G		intron_variant	Intron 5 of 11	ENST00000274793.12	NP_005075.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G7	ENST00000274793.12	c.470+118T>G		intron_variant	Intron 5 of 11	1	NM_005084.4	ENSP00000274793.7
PLA2G7	ENST00000537365.1	c.470+118T>G		intron_variant	Intron 5 of 11	1		ENSP00000445666.1

Frequencies

GnomAD3 genomes AF: 0.832 AC: 126359 AN: 151900 Hom.: 52751 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.832

GnomAD4 exome AF: 0.818 AC: 511275 AN: 624710 Hom.: 209776 AF XY: 0.820 AC XY: 278916 AN XY: 340056

African (AFR) AF: 0.888 AC: 15673 AN: 17640

American (AMR) AF: 0.851 AC: 36050 AN: 42362

Ashkenazi Jewish (ASJ) AF: 0.823 AC: 17183 AN: 20890

East Asian (EAS) AF: 0.887 AC: 31633 AN: 35668

South Asian (SAS) AF: 0.874 AC: 59851 AN: 68444

European-Finnish (FIN) AF: 0.746 AC: 32936 AN: 44126

Middle Eastern (MID) AF: 0.864 AC: 3582 AN: 4144

European-Non Finnish (NFE) AF: 0.802 AC: 287387 AN: 358372

Other (OTH) AF: 0.816 AC: 26980 AN: 33064

GnomAD4 genome AF: 0.832 AC: 126466 AN: 152016 Hom.: 52800 Cov.: 30 AF XY: 0.832 AC XY: 61834 AN XY: 74292

African (AFR) AF: 0.889 AC: 36876 AN: 41474

American (AMR) AF: 0.847 AC: 12919 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2842 AN: 3470

East Asian (EAS) AF: 0.885 AC: 4565 AN: 5160

South Asian (SAS) AF: 0.888 AC: 4282 AN: 4820

European-Finnish (FIN) AF: 0.754 AC: 7967 AN: 10562

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54464 AN: 67964

Other (OTH) AF: 0.832 AC: 1750 AN: 2104

Alfa AF: 0.811 Hom.: 138389

Bravo AF: 0.834

Asia WGS AF: 0.891 AC: 3099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.66
PhyloP100		-0.37
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: rs1362931; hg19: chr6-46682079;