Variant rs11573185 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_005245891.6(PLA2G5):c.-42C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 1,281,692 control chromosomes in the GnomAD database, including 179,473 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 0.46 ( 17261 hom., cov: 31)

Exomes 𝑓: 0.53 ( 162212 hom. )

Consequence

PLA2G5
XM_005245891.6 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

Variant links:

Genes affected

PLA2G5 (HGNC:9038): (phospholipase A2 group V) This gene is a member of the secretory phospholipase A2 family. It is located in a tightly-linked cluster of secretory phospholipase A2 genes on chromosome 1. The encoded enzyme catalyzes the hydrolysis of membrane phospholipids to generate lysophospholipids and free fatty acids including arachidonic acid. It preferentially hydrolyzes linoleoyl-containing phosphatidylcholine substrates. Secretion of this enzyme is thought to induce inflammatory responses in neighboring cells. Alternatively spliced transcript variants have been found, but their full-length nature has not been determined. [provided by RefSeq, Jul 2008]

PLA2G5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein
PLA2G5	XM_005245891.6 linkuse as main transcript	c.-42C>A	5_prime_UTR_variant	4/8	XP_005245948.1
PLA2G5	XM_005245892.6 linkuse as main transcript	c.-42C>A	5_prime_UTR_variant	3/7	XP_005245949.1
PLA2G5	XM_005245893.6 linkuse as main transcript	c.-307C>A	5_prime_UTR_variant	3/8	XP_005245950.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
PLA2G5	ENST00000460175.5 linkuse as main transcript	n.373C>A	non_coding_transcript_exon_variant	3/7	3
PLA2G5	ENST00000465698.5 linkuse as main transcript	n.377C>A	non_coding_transcript_exon_variant	3/8	3
PLA2G5	ENST00000469069.5 linkuse as main transcript	n.400C>A	non_coding_transcript_exon_variant	4/7	3

Frequencies

GnomAD3 genomes

AF:

0.457

AC:

69409

AN:

151870

Hom.:

17232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.556

Gnomad ASJ

AF:

0.484

Gnomad EAS

AF:

0.388

Gnomad SAS

AF:

0.480

Gnomad FIN

AF:

0.533

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.550

Gnomad OTH

AF:

0.483

GnomAD3 exomes

AF:

0.517

AC:

69057

AN:

133684

Hom.:

18479

AF XY:

0.518

AC XY:

37674

AN XY:

72780

show subpopulations

Gnomad AFR exome

AF:

0.234

Gnomad AMR exome

AF:

0.591

Gnomad ASJ exome

AF:

0.487

Gnomad EAS exome

AF:

0.371

Gnomad SAS exome

AF:

0.510

Gnomad FIN exome

AF:

0.553

Gnomad NFE exome

AF:

0.548

Gnomad OTH exome

AF:

0.536

GnomAD4 exome

AF:

0.532

AC:

600447

AN:

1129704

Hom.:

162212

Cov.:

AF XY:

0.532

AC XY:

294959

AN XY:

554636

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.592

Gnomad4 ASJ exome

AF:

0.492

Gnomad4 EAS exome

AF:

0.372

Gnomad4 SAS exome

AF:

0.505

Gnomad4 FIN exome

AF:

0.550

Gnomad4 NFE exome

AF:

0.543

Gnomad4 OTH exome

AF:

0.512

GnomAD4 genome

AF:

0.457

AC:

69490

AN:

151988

Hom.:

17261

Cov.:

AF XY:

0.457

AC XY:

33940

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.557

Gnomad4 ASJ

AF:

0.484

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.481

Gnomad4 FIN

AF:

0.533

Gnomad4 NFE

AF:

0.550

Gnomad4 OTH

AF:

0.488

Alfa

AF:

0.525

Hom.:

27275

Bravo

AF:

0.451

Asia WGS

AF:

0.447

AC:

1555

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.0

DANN

Benign

0.66

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over