dbSNP rs2284060: PLA2G6:c.210-1793A>G (chr22-38147446-T-C) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003560.4(PLA2G6):c.210-1793A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 168,824 control chromosomes in the GnomAD database, including 15,437 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.42 ( 13782 hom., cov: 30)

Exomes 𝑓: 0.43 ( 1655 hom. )

Consequence

PLA2G6
NM_003560.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.02

Variant links:

Genes affected

PLA2G6 (HGNC:9039): (phospholipase A2 group VI) The protein encoded by this gene is an A2 phospholipase, a class of enzyme that catalyzes the release of fatty acids from phospholipids. The encoded protein may play a role in phospholipid remodelling, arachidonic acid release, leukotriene and prostaglandin synthesis, fas-mediated apoptosis, and transmembrane ion flux in glucose-stimulated B-cells. Several transcript variants encoding multiple isoforms have been described, but the full-length nature of only three of them have been determined to date. [provided by RefSeq, Dec 2010]

PLA2G6 links:

ENSG00000279080 (HGNC:):

ENSG00000279080 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 22-38147446-T-C is Benign according to our data. Variant chr22-38147446-T-C is described in ClinVar as [Benign]. Clinvar id is 3255255.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr22-38147446-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G6	NM_003560.4 link	c.210-1793A>G		intron_variant	Intron 2 of 16	ENST00000332509.8	NP_003551.2	O60733-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G6	ENST00000332509.8 link	c.210-1793A>G		intron_variant	Intron 2 of 16	1	NM_003560.4	ENSP00000333142.3		O60733-1

Frequencies

GnomAD3 genomes

AF:

0.421

AC:

63907

AN:

151628

Hom.:

13771

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.480

Gnomad AMR

AF:

0.454

Gnomad ASJ

AF:

0.492

Gnomad EAS

AF:

0.326

Gnomad SAS

AF:

0.546

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.475

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.425

GnomAD4 exome

AF:

0.433

AC:

7394

AN:

17078

Hom.:

1655

Cov.:

AF XY:

0.435

AC XY:

3546

AN XY:

8158

show subpopulations

Gnomad4 AFR exome

AF:

0.359

AC:

AN:

Gnomad4 AMR exome

AF:

0.500

AC:

AN:

Gnomad4 ASJ exome

AF:

0.500

AC:

AN:

Gnomad4 EAS exome

AF:

0.250

AC:

AN:

Gnomad4 SAS exome

AF:

0.500

AC:

AN:

Gnomad4 FIN exome

AF:

0.428

AC:

6285

AN:

14700

Gnomad4 NFE exome

AF:

0.433

AC:

117

AN:

270

Gnomad4 Remaining exome

AF:

0.479

AC:

135

AN:

282

Heterozygous variant carriers

207

414

622

829

1036

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

110

<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:

0.422

AC:

63971

AN:

151746

Hom.:

13782

Cov.:

AF XY:

0.424

AC XY:

31454

AN XY:

74118

show subpopulations

Gnomad4 AFR

AF:

0.381

AC:

0.380519

AN:

0.380519

Gnomad4 AMR

AF:

0.454

AC:

0.454193

AN:

0.454193

Gnomad4 ASJ

AF:

0.492

AC:

0.492197

AN:

0.492197

Gnomad4 EAS

AF:

0.326

AC:

0.326499

AN:

0.326499

Gnomad4 SAS

AF:

0.545

AC:

0.54536

AN:

0.54536

Gnomad4 FIN

AF:

0.416

AC:

0.416492

AN:

0.416492

Gnomad4 NFE

AF:

0.434

AC:

0.433657

AN:

0.433657

Gnomad4 OTH

AF:

0.428

AC:

0.428232

AN:

0.428232

Heterozygous variant carriers

1862

3724

5587

7449

9311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

604

1208

1812

2416

3020

<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:

0.433

Hom.:

35399

Bravo

AF:

0.416

Asia WGS

AF:

0.469

AC:

1634

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jul 15, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 63% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 59. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.32

DANN

Benign

0.49

Mutation Taster

=100/0

polymorphism (auto)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.12

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over