Genetic Variant PLA2G5:n.373C>G (chr1-20068908-C-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000460175.5(PLA2G5):n.373C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,286,040 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00067 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000073 ( 0 hom. )

Consequence

PLA2G5
ENST00000460175.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.229

Publications

7 publications found

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 Gene-Disease associations (from GenCC):

familial benign flecked retina
Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE, LIMITED Submitted by: G2P, Ambry Genetics, Orphanet
late-adult onset retinitis pigmentosa
Inheritance: AR Classification: LIMITED Submitted by: Franklin by Genoox

PLA2G5 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
PLA2G5	XM_005245891.6 link	c.-42C>G	5_prime_UTR_variant	Exon 4 of 8	XP_005245948.1
PLA2G5	XM_005245892.6 link	c.-42C>G	5_prime_UTR_variant	Exon 3 of 7	XP_005245949.1
PLA2G5	XM_011541586.4 link	c.-42C>G	5_prime_UTR_variant	Exon 2 of 6	XP_011539888.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PLA2G5	ENST00000460175.5 link	n.373C>G	non_coding_transcript_exon_variant	Exon 3 of 7	3
PLA2G5	ENST00000465698.5 link	n.377C>G	non_coding_transcript_exon_variant	Exon 3 of 8	3
PLA2G5	ENST00000469069.5 link	n.400C>G	non_coding_transcript_exon_variant	Exon 4 of 7	3

Frequencies

GnomAD3 genomes

AF:

0.000671

AC:

102

AN:

151940

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00235

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.000478

GnomAD2 exomes

AF:

0.000180

AC:

AN:

133684

AF XY:

0.000137

show subpopulations

Gnomad AFR exome

AF:

0.00202

Gnomad AMR exome

AF:

0.000205

Gnomad ASJ exome

AF:

0.000121

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000382

Gnomad OTH exome

AF:

0.000243

GnomAD4 exome

AF:

0.0000732

AC:

AN:

1133982

Hom.:

Cov.:

AF XY:

0.0000647

AC XY:

AN XY:

556532

show subpopulations

African (AFR)

AF:

0.00209

AC:

AN:

24354

American (AMR)

AF:

0.000284

AC:

AN:

28212

Ashkenazi Jewish (ASJ)

AF:

0.0000629

AC:

AN:

15892

East Asian (EAS)

AF:

0.00

AC:

AN:

12826

South Asian (SAS)

AF:

0.0000658

AC:

AN:

76044

European-Finnish (FIN)

AF:

0.00

AC:

AN:

13066

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4398

European-Non Finnish (NFE)

AF:

0.0000174

AC:

AN:

917750

Other (OTH)

AF:

0.0000483

AC:

AN:

41440

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000671

AC:

102

AN:

152058

Hom.:

Cov.:

AF XY:

0.000700

AC XY:

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.00234

AC:

AN:

41476

American (AMR)

AF:

0.000131

AC:

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.000194

AC:

AN:

5160

South Asian (SAS)

AF:

0.000208

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10534

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67992

Other (OTH)

AF:

0.000473

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

37477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.66

(source)

DANN

Benign

0.56

PhyloP100

-0.23

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over