rs563112904

Variant names:

• chr15-42086199-A-C
• rs563112904
• NM_178034.4:c.387+14T>G

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_178034.4(PLA2G4D):​c.387+14T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.37 (0 hom., cov: 0)
  • Exomes 𝑓: 0.42 (2127 hom.)
  • Failed GnomAD Quality Control
• Consequence: PLA2G4D NM_178034.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.436
• Publications: 0 publications found

Genes affected

PLA2G4D (HGNC:30038): (phospholipase A2 group IVD) The phospholipase A2 enzyme family, including PLA2G4D, catalyze the hydrolysis of glycerophospholipids at the sn-2 position and then liberate free fatty acids and lysophospholipids (Chiba et al., 2004 [PubMed 14709560]).[supplied by OMIM, Jun 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 15-42086199-A-C is Benign according to our data. Variant chr15-42086199-A-C is described in ClinVar as Benign. ClinVar VariationId is 403315.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLA2G4D	NM_178034.4	c.387+14T>G		intron_variant	Intron 4 of 19	ENST00000290472.4	NP_828848.3
PLA2G4D	XM_047432399.1	c.387+14T>G		intron_variant	Intron 4 of 19		XP_047288355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLA2G4D	ENST00000290472.4	c.387+14T>G		intron_variant	Intron 4 of 19	1	NM_178034.4	ENSP00000290472.3

Frequencies

GnomAD3 genomes AF: 0.372 AC: 21101 AN: 56670 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.373

GnomAD2 exomes AF: 0.471 AC: 27614 AN: 58584 AF XY: 0.475

Gnomad AFR exome AF: 0.429

Gnomad AMR exome AF: 0.488

Gnomad ASJ exome AF: 0.496

Gnomad EAS exome AF: 0.408

Gnomad FIN exome AF: 0.482

Gnomad NFE exome AF: 0.468

Gnomad OTH exome AF: 0.470

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.424 AC: 69095 AN: 162910 Hom.: 2127 Cov.: 0 AF XY: 0.431 AC XY: 38297 AN XY: 88826

African (AFR) AF: 0.419 AC: 1293 AN: 3086

American (AMR) AF: 0.543 AC: 5520 AN: 10166

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 2100 AN: 4232

East Asian (EAS) AF: 0.419 AC: 1965 AN: 4692

South Asian (SAS) AF: 0.472 AC: 12905 AN: 27350

European-Finnish (FIN) AF: 0.476 AC: 5341 AN: 11228

Middle Eastern (MID) AF: 0.448 AC: 248 AN: 554

European-Non Finnish (NFE) AF: 0.388 AC: 36637 AN: 94414

Other (OTH) AF: 0.429 AC: 3086 AN: 7188

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.372 AC: 21104 AN: 56690 Hom.: 0 Cov.: 0 AF XY: 0.351 AC XY: 9251 AN XY: 26354

African (AFR) AF: 0.358 AC: 5512 AN: 15386

American (AMR) AF: 0.306 AC: 1700 AN: 5550

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 531 AN: 1288

East Asian (EAS) AF: 0.349 AC: 441 AN: 1262

South Asian (SAS) AF: 0.339 AC: 346 AN: 1022

European-Finnish (FIN) AF: 0.176 AC: 537 AN: 3058

Middle Eastern (MID) AF: 0.343 AC: 24 AN: 70

European-Non Finnish (NFE) AF: 0.415 AC: 11589 AN: 27942

Other (OTH) AF: 0.372 AC: 292 AN: 786

Alfa AF: 0.0188 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	15
DANN	Benign	0.71
PhyloP100		0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs563112904; hg19: chr15-42378397; COSMIC: COSV106055772; COSMIC: COSV106055772;